Starting phenix.real_space_refine
on Wed Mar 20 22:38:35 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8reb_19081/03_2024/8reb_19081.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8reb_19081/03_2024/8reb_19081.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8reb_19081/03_2024/8reb_19081.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8reb_19081/03_2024/8reb_19081.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8reb_19081/03_2024/8reb_19081.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8reb_19081/03_2024/8reb_19081.pdb"
  }
  resolution = 3.4
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     101      5.49       5
     Mg      1      5.21       5
     S      98      5.16       5
     C   17684      2.51       5
     N    5093      2.21       5
     O    5702      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU   17": "OE1" <-> "OE2"
    Residue "A ASP   62": "OD1" <-> "OD2"
    Residue "A GLU   72": "OE1" <-> "OE2"
    Residue "A GLU  122": "OE1" <-> "OE2"
    Residue "A TYR  152": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  181": "OE1" <-> "OE2"
    Residue "A ASP  199": "OD1" <-> "OD2"
    Residue "A GLU  204": "OE1" <-> "OE2"
    Residue "A ASP  212": "OD1" <-> "OD2"
    Residue "A GLU  214": "OE1" <-> "OE2"
    Residue "A GLU  215": "OE1" <-> "OE2"
    Residue "A PHE  231": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  250": "OD1" <-> "OD2"
    Residue "A ASP  258": "OD1" <-> "OD2"
    Residue "A GLU  273": "OE1" <-> "OE2"
    Residue "A TYR  277": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  288": "OE1" <-> "OE2"
    Residue "B GLU    7": "OE1" <-> "OE2"
    Residue "B GLU   76": "OE1" <-> "OE2"
    Residue "B ASP   77": "OD1" <-> "OD2"
    Residue "B ASP   96": "OD1" <-> "OD2"
    Residue "B ASP  118": "OD1" <-> "OD2"
    Residue "B ASP  120": "OD1" <-> "OD2"
    Residue "B GLU  229": "OE1" <-> "OE2"
    Residue "C TYR    5": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU    7": "OE1" <-> "OE2"
    Residue "C ASP   14": "OD1" <-> "OD2"
    Residue "C ASP   23": "OD1" <-> "OD2"
    Residue "C TYR   26": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR   62": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU   67": "OE1" <-> "OE2"
    Residue "C TYR   70": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  132": "OD1" <-> "OD2"
    Residue "C PHE  136": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  186": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  188": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  189": "OD1" <-> "OD2"
    Residue "C PHE  195": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  215": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  346": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  365": "OE1" <-> "OE2"
    Residue "C GLU  382": "OE1" <-> "OE2"
    Residue "C ASP  393": "OD1" <-> "OD2"
    Residue "C ASP  434": "OD1" <-> "OD2"
    Residue "C GLU  472": "OE1" <-> "OE2"
    Residue "C GLU  504": "OE1" <-> "OE2"
    Residue "C GLU  546": "OE1" <-> "OE2"
    Residue "C GLU  588": "OE1" <-> "OE2"
    Residue "C ASP  596": "OD1" <-> "OD2"
    Residue "C TYR  605": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  624": "OD1" <-> "OD2"
    Residue "C GLU  625": "OE1" <-> "OE2"
    Residue "C GLU  641": "OE1" <-> "OE2"
    Residue "C ASP  675": "OD1" <-> "OD2"
    Residue "C ASP  696": "OD1" <-> "OD2"
    Residue "C GLU  705": "OE1" <-> "OE2"
    Residue "C ASP  711": "OD1" <-> "OD2"
    Residue "C TYR  726": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  738": "OE1" <-> "OE2"
    Residue "C ASP  739": "OD1" <-> "OD2"
    Residue "C TYR  742": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  751": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  825": "OE1" <-> "OE2"
    Residue "C ASP  853": "OD1" <-> "OD2"
    Residue "C ASP  866": "OD1" <-> "OD2"
    Residue "C GLU  876": "OE1" <-> "OE2"
    Residue "C GLU  940": "OE1" <-> "OE2"
    Residue "C GLU 1020": "OE1" <-> "OE2"
    Residue "C GLU 1030": "OE1" <-> "OE2"
    Residue "C ASP 1041": "OD1" <-> "OD2"
    Residue "C TYR 1053": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU 1083": "OE1" <-> "OE2"
    Residue "C ASP 1095": "OD1" <-> "OD2"
    Residue "C GLU 1143": "OE1" <-> "OE2"
    Residue "C ASP 1160": "OD1" <-> "OD2"
    Residue "C GLU 1167": "OE1" <-> "OE2"
    Residue "C ASP 1203": "OD1" <-> "OD2"
    Residue "C GLU 1219": "OE1" <-> "OE2"
    Residue "C ASP 1241": "OD1" <-> "OD2"
    Residue "C PHE 1265": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP 1310": "OD1" <-> "OD2"
    Residue "C GLU 1316": "OE1" <-> "OE2"
    Residue "D PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU   15": "OE1" <-> "OE2"
    Residue "D ASP   28": "OD1" <-> "OD2"
    Residue "D PHE   35": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ASP   54": "OD1" <-> "OD2"
    Residue "D TYR   75": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU   86": "OE1" <-> "OE2"
    Residue "D GLU   91": "OE1" <-> "OE2"
    Residue "D PHE  116": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ASP  134": "OD1" <-> "OD2"
    Residue "D GLU  142": "OE1" <-> "OE2"
    Residue "D GLU  203": "OE1" <-> "OE2"
    Residue "D GLU  225": "OE1" <-> "OE2"
    Residue "D GLU  235": "OE1" <-> "OE2"
    Residue "D PHE  260": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR  269": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ASP  348": "OD1" <-> "OD2"
    Residue "D ASP  413": "OD1" <-> "OD2"
    Residue "D GLU  414": "OE1" <-> "OE2"
    Residue "D GLU  479": "OE1" <-> "OE2"
    Residue "D GLU  497": "OE1" <-> "OE2"
    Residue "D GLU  562": "OE1" <-> "OE2"
    Residue "D GLU  656": "OE1" <-> "OE2"
    Residue "D GLU  658": "OE1" <-> "OE2"
    Residue "D GLU  660": "OE1" <-> "OE2"
    Residue "D GLU  666": "OE1" <-> "OE2"
    Residue "D PHE  668": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ASP  699": "OD1" <-> "OD2"
    Residue "D GLU  714": "OE1" <-> "OE2"
    Residue "D PHE  719": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ASP  727": "OD1" <-> "OD2"
    Residue "D GLU  765": "OE1" <-> "OE2"
    Residue "D GLU  811": "OE1" <-> "OE2"
    Residue "D GLU  818": "OE1" <-> "OE2"
    Residue "D GLU  827": "OE1" <-> "OE2"
    Residue "D ASP  830": "OD1" <-> "OD2"
    Residue "D GLU  833": "OE1" <-> "OE2"
    Residue "D ASP  837": "OD1" <-> "OD2"
    Residue "D GLU  846": "OE1" <-> "OE2"
    Residue "D TYR  899": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU 1146": "OE1" <-> "OE2"
    Residue "D GLU 1152": "OE1" <-> "OE2"
    Residue "D GLU 1187": "OE1" <-> "OE2"
    Residue "D GLU 1188": "OE1" <-> "OE2"
    Residue "D ASP 1219": "OD1" <-> "OD2"
    Residue "D TYR 1232": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU 1236": "OE1" <-> "OE2"
    Residue "D ASP 1250": "OD1" <-> "OD2"
    Residue "D GLU 1276": "OE1" <-> "OE2"
    Residue "D GLU 1334": "OE1" <-> "OE2"
    Residue "D GLU 1343": "OE1" <-> "OE2"
    Residue "D TYR 1365": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ASP   65": "OD1" <-> "OD2"
    Residue "M GLU  173": "OE1" <-> "OE2"
    Residue "M TYR  401": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M PHE  402": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.08s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 28681
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "N"
      Number of atoms: 875
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 875
          Classifications: {'DNA': 43}
          Link IDs: {'rna3p': 42}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 129
          Classifications: {'RNA': 6}
          Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 3}
          Link IDs: {'rna3p': 5}
    Chain: "T"
      Number of atoms: 1072
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 1072
          Classifications: {'DNA': 52}
          Link IDs: {'rna3p': 51}
    Chain: "A"
      Number of atoms: 2365
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2365
          Classifications: {'peptide': 308}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 14, 'TRANS': 293}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 22
    Chain: "B"
      Number of atoms: 1735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1735
          Classifications: {'peptide': 235}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225}
          Unresolved non-hydrogen bonds: 93
          Unresolved non-hydrogen angles: 115
          Unresolved non-hydrogen dihedrals: 78
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 5, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 75
    Chain: "C"
      Number of atoms: 10080
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1341, 10080
          Classifications: {'peptide': 1341}
          Incomplete info: {'truncation_to_alanine': 118}
          Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 509
          Unresolved non-hydrogen angles: 619
          Unresolved non-hydrogen dihedrals: 432
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 22, 'ARG:plan': 18}
          Unresolved non-hydrogen planarities: 338
    Chain: "D"
      Number of atoms: 9682
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1330, 9682
          Classifications: {'peptide': 1330}
          Incomplete info: {'truncation_to_alanine': 172}
          Link IDs: {'PTRANS': 53, 'TRANS': 1276}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 691
          Unresolved non-hydrogen angles: 840
          Unresolved non-hydrogen dihedrals: 585
          Unresolved non-hydrogen chiralities: 23
          Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 9, 'GLU:plan': 31, 'ARG:plan': 18}
          Unresolved non-hydrogen planarities: 441
    Chain: "E"
      Number of atoms: 546
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 546
          Classifications: {'peptide': 74}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 2, 'TRANS': 71}
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 55
          Unresolved non-hydrogen dihedrals: 35
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 40
    Chain: "M"
      Number of atoms: 2194
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 350, 2194
          Classifications: {'peptide': 350}
          Incomplete info: {'truncation_to_alanine': 176}
          Link IDs: {'PTRANS': 15, 'TRANS': 334}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 582
          Unresolved non-hydrogen angles: 739
          Unresolved non-hydrogen dihedrals: 457
          Unresolved non-hydrogen chiralities: 55
          Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 10, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 22, 'PHE:plan': 2, 'GLU:plan': 26, 'HIS:plan': 4}
          Unresolved non-hydrogen planarities: 341
    Chain: "D"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' MG': 1, ' ZN': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  16779  SG  CYS D  70     106.543 114.667  92.090  1.00 66.62           S
  ATOM  16908  SG  CYS D  88     104.966 114.784  95.832  1.00 66.10           S
  ATOM  22401  SG  CYS D 814     100.730  47.899  85.807  1.00 47.44           S
  ATOM  23021  SG  CYS D 898      98.212  47.559  85.093  1.00 25.73           S

  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   GLY M 166 " occ=0.71
      ... (2 atoms not shown)
      pdb=" O   GLY M 166 " occ=0.71
  Time building chain proxies: 14.76, per 1000 atoms: 0.51
  Number of scatterers: 28681
  At special positions: 0
  Unit cell: (140.98, 172.78, 166.42, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      2     29.99
     S      98     16.00
     P     101     15.00
     Mg      1     11.99
     O    5702      8.00
     N    5093      7.00
     C   17684      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 11.18
  Conformation dependent library (CDL) restraints added in 5.3 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN D1502 "
        pdb="ZN    ZN D1502 " - pdb=" SG  CYS D  88 "
        pdb="ZN    ZN D1502 " - pdb=" SG  CYS D  70 "
      pdb="  ZN D1503 "
        pdb="ZN    ZN D1503 " - pdb=" SG  CYS D 898 "
        pdb="ZN    ZN D1503 " - pdb=" SG  CYS D 814 "


  7224 Ramachandran restraints generated.
    3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  6748

  Finding SS restraints...
    Secondary structure from input PDB file:
      125 helices and 45 sheets defined
      39.3% alpha, 14.2% beta
      40 base pairs and 81 stacking pairs defined.
    Time for finding SS restraints: 9.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 50
      removed outlier: 3.857A  pdb=" N   THR A  38 " --> pdb=" O   GLY A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 87
      removed outlier: 3.743A  pdb=" N   GLY A  87 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 115
      No H-bonds generated for 'chain 'A' and resid 113 through 115'
    Processing helix  chain 'A' and resid 159 through 164
      removed outlier: 3.957A  pdb=" N   ASP A 164 " --> pdb=" O   SER A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 229
    Processing helix  chain 'A' and resid 263 through 273
      removed outlier: 4.018A  pdb=" N   ASN A 268 " --> pdb=" O   VAL A 264 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   CYS A 269 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 282
      removed outlier: 3.592A  pdb=" N   LEU A 281 " --> pdb=" O   TYR A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 290
    Processing helix  chain 'A' and resid 296 through 309
    Processing helix  chain 'B' and resid 34 through 50
      removed outlier: 3.773A  pdb=" N   THR B  38 " --> pdb=" O   GLY B  34 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   SER B  50 " --> pdb=" O   ILE B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 74
      removed outlier: 3.832A  pdb=" N   GLY B  73 " --> pdb=" O   THR B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 88
      removed outlier: 3.663A  pdb=" N   GLY B  87 " --> pdb=" O   LEU B  83 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   LEU B  88 " --> pdb=" O   ASN B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 115
      No H-bonds generated for 'chain 'B' and resid 113 through 115'
    Processing helix  chain 'B' and resid 164 through 169
    Processing helix  chain 'B' and resid 212 through 227
    Processing helix  chain 'B' and resid 228 through 233
    Processing helix  chain 'C' and resid 4 through 9
      removed outlier: 3.689A  pdb=" N   LYS C   9 " --> pdb=" O   TYR C   5 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 40
    Processing helix  chain 'C' and resid 48 through 57
    Processing helix  chain 'C' and resid 81 through 89
    Processing helix  chain 'C' and resid 159 through 163
      removed outlier: 3.738A  pdb=" N   LYS C 163 " --> pdb=" O   ASP C 160 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 206 through 213
      removed outlier: 4.196A  pdb=" N   LEU C 210 " --> pdb=" O   ALA C 206 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 216 through 225
    Processing helix  chain 'C' and resid 270 through 280
    Processing helix  chain 'C' and resid 290 through 294
      removed outlier: 3.544A  pdb=" N   GLY C 294 " --> pdb=" O   TYR C 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 318 through 329
    Processing helix  chain 'C' and resid 347 through 354
    Processing helix  chain 'C' and resid 358 through 371
    Processing helix  chain 'C' and resid 379 through 389
    Processing helix  chain 'C' and resid 398 through 409
    Processing helix  chain 'C' and resid 422 through 438
      removed outlier: 4.018A  pdb=" N   ILE C 426 " --> pdb=" O   LYS C 422 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 455 through 479
      removed outlier: 3.605A  pdb=" N   ALA C 474 " --> pdb=" O   ARG C 470 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   GLU C 477 " --> pdb=" O   ARG C 473 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   ARG C 478 " --> pdb=" O   ALA C 474 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   LEU C 479 " --> pdb=" O   VAL C 475 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 480 through 482
      No H-bonds generated for 'chain 'C' and resid 480 through 482'
    Processing helix  chain 'C' and resid 494 through 508
      removed outlier: 4.330A  pdb=" N   ILE C 498 " --> pdb=" O   ASN C 494 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 518 through 528
      removed outlier: 3.593A  pdb=" N   SER C 522 " --> pdb=" O   ASN C 518 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   GLU C 523 " --> pdb=" O   ASN C 519 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 551 through 555
      removed outlier: 3.963A  pdb=" N   TYR C 555 " --> pdb=" O   PRO C 552 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 609 through 613
      removed outlier: 3.529A  pdb=" N   ASN C 613 " --> pdb=" O   GLU C 610 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 664 through 668
      removed outlier: 3.631A  pdb=" N   LEU C 667 " --> pdb=" O   GLY C 664 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ILE C 668 " --> pdb=" O   ALA C 665 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 664 through 668'
    Processing helix  chain 'C' and resid 670 through 674
    Processing helix  chain 'C' and resid 675 through 687
      removed outlier: 4.106A  pdb=" N   ARG C 687 " --> pdb=" O   ALA C 683 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 704 through 712
    Processing helix  chain 'C' and resid 820 through 825
    Processing helix  chain 'C' and resid 860 through 865
      removed outlier: 4.146A  pdb=" N   LYS C 864 " --> pdb=" O   ALA C 861 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 896 through 906
    Processing helix  chain 'C' and resid 942 through 982
      removed outlier: 3.805A  pdb=" N   GLU C 947 " --> pdb=" O   LYS C 943 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   GLU C 962 " --> pdb=" O   LYS C 958 " (cutoff:3.500A)
      removed outlier: 5.037A  pdb=" N   GLU C 963 " --> pdb=" O   ASP C 959 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LEU C 964 " --> pdb=" O   LEU C 960 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 986 through 992
    Processing helix  chain 'C' and resid 993 through 1000
      removed outlier: 3.729A  pdb=" N   TRP C 997 " --> pdb=" O   PRO C 993 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   LEU C1000 " --> pdb=" O   ARG C 996 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1003 through 1009
    Processing helix  chain 'C' and resid 1009 through 1037
    Processing helix  chain 'C' and resid 1081 through 1085
    Processing helix  chain 'C' and resid 1099 through 1103
    Processing helix  chain 'C' and resid 1108 through 1134
      removed outlier: 4.299A  pdb=" N   ILE C1112 " --> pdb=" O   ASN C1108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1137 through 1150
      removed outlier: 3.708A  pdb=" N   LEU C1141 " --> pdb=" O   GLU C1137 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1165 through 1176
    Processing helix  chain 'C' and resid 1191 through 1202
    Processing helix  chain 'C' and resid 1238 through 1242
    Processing helix  chain 'C' and resid 1271 through 1282
    Processing helix  chain 'C' and resid 1283 through 1292
    Processing helix  chain 'C' and resid 1297 through 1311
      removed outlier: 3.954A  pdb=" N   THR C1302 " --> pdb=" O   VAL C1298 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1320 through 1332
      removed outlier: 3.519A  pdb=" N   ASN C1324 " --> pdb=" O   PRO C1320 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 26 through 34
    Processing helix  chain 'D' and resid 70 through 74
      removed outlier: 4.079A  pdb=" N   LYS D  74 " --> pdb=" O   LEU D  71 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 96 through 100
    Processing helix  chain 'D' and resid 113 through 118
    Processing helix  chain 'D' and resid 122 through 128
    Processing helix  chain 'D' and resid 131 through 140
      removed outlier: 3.588A  pdb=" N   ILE D 135 " --> pdb=" O   PRO D 131 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 161 through 172
    Processing helix  chain 'D' and resid 181 through 191
      removed outlier: 3.765A  pdb=" N   ILE D 185 " --> pdb=" O   GLY D 181 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 193 through 208
    Processing helix  chain 'D' and resid 210 through 231
      removed outlier: 3.707A  pdb=" N   LYS D 215 " --> pdb=" O   GLU D 211 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   LYS D 216 " --> pdb=" O   THR D 212 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLY D 231 " --> pdb=" O   PHE D 227 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 233 through 237
    Processing helix  chain 'D' and resid 246 through 250
    Processing helix  chain 'D' and resid 263 through 284
      removed outlier: 3.949A  pdb=" N   ASP D 284 " --> pdb=" O   LYS D 280 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 288 through 308
    Processing helix  chain 'D' and resid 377 through 388
    Processing helix  chain 'D' and resid 393 through 404
    Processing helix  chain 'D' and resid 405 through 417
      removed outlier: 3.790A  pdb=" N   ARG D 417 " --> pdb=" O   ASP D 413 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 430 through 432
      No H-bonds generated for 'chain 'D' and resid 430 through 432'
    Processing helix  chain 'D' and resid 453 through 458
    Processing helix  chain 'D' and resid 473 through 483
    Processing helix  chain 'D' and resid 504 through 514
    Processing helix  chain 'D' and resid 529 through 539
    Processing helix  chain 'D' and resid 574 through 581
      removed outlier: 3.786A  pdb=" N   MET D 581 " --> pdb=" O   ALA D 577 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 588 through 592
    Processing helix  chain 'D' and resid 599 through 612
    Processing helix  chain 'D' and resid 614 through 636
    Processing helix  chain 'D' and resid 649 through 670
    Processing helix  chain 'D' and resid 674 through 703
      removed outlier: 4.172A  pdb=" N   THR D 703 " --> pdb=" O   ASP D 699 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 720 through 728
    Processing helix  chain 'D' and resid 733 through 741
    Processing helix  chain 'D' and resid 768 through 805
      removed outlier: 3.755A  pdb=" N   HIS D 777 " --> pdb=" O   PHE D 773 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   GLY D 778 " --> pdb=" O   ILE D 774 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   THR D 790 " --> pdb=" O   THR D 786 " (cutoff:3.500A)
      removed outlier: 4.788A  pdb=" N   ALA D 791 " --> pdb=" O   ALA D 787 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   ASN D 792 " --> pdb=" O   LEU D 788 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 834 through 840
    Processing helix  chain 'D' and resid 865 through 875
    Processing helix  chain 'D' and resid 884 through 888
      removed outlier: 3.622A  pdb=" N   CYS D 888 " --> pdb=" O   VAL D 885 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 914 through 925
      removed outlier: 3.739A  pdb=" N   ILE D 918 " --> pdb=" O   ALA D 914 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1140 through 1146
    Processing helix  chain 'D' and resid 1216 through 1224
    Processing helix  chain 'D' and resid 1225 through 1245
      removed outlier: 3.543A  pdb=" N   VAL D1229 " --> pdb=" O   GLY D1225 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   VAL D1240 " --> pdb=" O   GLU D1236 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   GLN D1244 " --> pdb=" O   VAL D1240 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1250 through 1259
      removed outlier: 3.743A  pdb=" N   ILE D1256 " --> pdb=" O   HIS D1252 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1279 through 1293
    Processing helix  chain 'D' and resid 1295 through 1299
      removed outlier: 3.743A  pdb=" N   VAL D1298 " --> pdb=" O   ASN D1295 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1308 through 1314
      removed outlier: 3.961A  pdb=" N   LEU D1314 " --> pdb=" O   THR D1310 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1327 through 1339
      removed outlier: 3.551A  pdb=" N   VAL D1331 " --> pdb=" O   GLU D1327 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1346 through 1353
      removed outlier: 3.991A  pdb=" N   ASN D1350 " --> pdb=" O   GLY D1346 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1360 through 1376
      removed outlier: 4.170A  pdb=" N   ALA D1364 " --> pdb=" O   GLY D1360 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   TYR D1365 " --> pdb=" O   THR D1361 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ASP D1368 " --> pdb=" O   ALA D1364 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 6 through 13
    Processing helix  chain 'E' and resid 17 through 33
      removed outlier: 4.019A  pdb=" N   LEU E  21 " --> pdb=" O   PHE E  17 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   GLY E  33 " --> pdb=" O   GLN E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 45 through 56
    Processing helix  chain 'E' and resid 60 through 75
    Processing helix  chain 'M' and resid 119 through 130
      removed outlier: 3.539A  pdb=" N   LEU M 130 " --> pdb=" O   TRP M 126 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 134 through 147
      removed outlier: 3.740A  pdb=" N   ALA M 147 " --> pdb=" O   SER M 143 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 157 through 166
    Processing helix  chain 'M' and resid 171 through 183
    Processing helix  chain 'M' and resid 194 through 205
      removed outlier: 3.633A  pdb=" N   GLN M 205 " --> pdb=" O   ILE M 201 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 212 through 218
      removed outlier: 4.033A  pdb=" N   LEU M 218 " --> pdb=" O   GLU M 214 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 224 through 230
    Processing helix  chain 'M' and resid 234 through 240
    Processing helix  chain 'M' and resid 242 through 255
      removed outlier: 3.538A  pdb=" N   GLU M 248 " --> pdb=" O   GLU M 244 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ASN M 251 " --> pdb=" O   LYS M 247 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 325 through 351
    Processing helix  chain 'M' and resid 351 through 356
      removed outlier: 4.295A  pdb=" N   PHE M 355 " --> pdb=" O   GLN M 351 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 366 through 375
      removed outlier: 3.556A  pdb=" N   ILE M 370 " --> pdb=" O   VAL M 366 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 377 through 385
    Processing helix  chain 'M' and resid 416 through 430
    Processing helix  chain 'M' and resid 438 through 450
    Processing helix  chain 'M' and resid 454 through 466
      removed outlier: 3.895A  pdb=" N   VAL M 458 " --> pdb=" O   ALA M 454 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ALA M 459 " --> pdb=" O   ARG M 455 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   LEU M 465 " --> pdb=" O   TYR M 461 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17
      removed outlier: 8.777A  pdb=" N   LEU A  13 " --> pdb=" O   GLU A  29 " (cutoff:3.500A)
      removed outlier: 7.135A  pdb=" N   GLU A  29 " --> pdb=" O   LEU A  13 " (cutoff:3.500A)
      removed outlier: 5.022A  pdb=" N   ASP A  15 " --> pdb=" O   THR A  27 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   THR A  27 " --> pdb=" O   ASP A  15 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   ASP A 199 " --> pdb=" O   PRO A  30 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105
      removed outlier: 3.702A  pdb=" N   GLU A  58 " --> pdb=" O   LYS A 145 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   GLN A 147 " --> pdb=" O   VAL A  56 " (cutoff:3.500A)
      removed outlier: 5.428A  pdb=" N   VAL A  56 " --> pdb=" O   GLN A 147 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   GLY A 149 " --> pdb=" O   CYS A  54 " (cutoff:3.500A)
      removed outlier: 5.225A  pdb=" N   CYS A  54 " --> pdb=" O   GLY A 149 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92
    Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111
      removed outlier: 3.599A  pdb=" N   CYS A 131 " --> pdb=" O   VAL A 110 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 19
      removed outlier: 6.513A  pdb=" N   ASP B 199 " --> pdb=" O   PRO B  30 " (cutoff:3.500A)
      removed outlier: 4.908A  pdb=" N   THR B 196 " --> pdb=" O   VAL B 192 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   VAL B 192 " --> pdb=" O   THR B 196 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 61
      removed outlier: 3.982A  pdb=" N   ALA B  55 " --> pdb=" O   GLN B 147 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   GLN B 147 " --> pdb=" O   ALA B  55 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   LYS B 145 " --> pdb=" O   THR B  57 " (cutoff:3.500A)
      removed outlier: 4.676A  pdb=" N   VAL B  59 " --> pdb=" O   ARG B 143 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   ARG B 143 " --> pdb=" O   VAL B  59 " (cutoff:3.500A)
      removed outlier: 5.122A  pdb=" N   ILE B  61 " --> pdb=" O   SER B 141 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   SER B 141 " --> pdb=" O   ILE B  61 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92
    Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 111
      removed outlier: 3.541A  pdb=" N   CYS B 131 " --> pdb=" O   VAL B 110 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 152 through 153
    Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14
      removed outlier: 5.822A  pdb=" N   LYS C  13 " --> pdb=" O   ALA C1183 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60
      removed outlier: 3.941A  pdb=" N   ILE C  59 " --> pdb=" O   LEU C  68 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU C  68 " --> pdb=" O   ILE C  59 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   SER C  66 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   TYR C 105 " --> pdb=" O   SER C  66 " (cutoff:3.500A)
      removed outlier: 5.548A  pdb=" N   LEU C  68 " --> pdb=" O   VAL C 103 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   VAL C 103 " --> pdb=" O   LEU C  68 " (cutoff:3.500A)
      removed outlier: 5.539A  pdb=" N   TYR C  70 " --> pdb=" O   ARG C 101 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   ARG C 101 " --> pdb=" O   TYR C  70 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   SER C  72 " --> pdb=" O   LYS C  99 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   LEU C 102 " --> pdb=" O   ASP C 116 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   ASP C 116 " --> pdb=" O   LEU C 102 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   ILE C 104 " --> pdb=" O   VAL C 114 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60
      removed outlier: 3.941A  pdb=" N   ILE C  59 " --> pdb=" O   LEU C  68 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU C  68 " --> pdb=" O   ILE C  59 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   SER C  66 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   TYR C 105 " --> pdb=" O   SER C  66 " (cutoff:3.500A)
      removed outlier: 5.548A  pdb=" N   LEU C  68 " --> pdb=" O   VAL C 103 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   VAL C 103 " --> pdb=" O   LEU C  68 " (cutoff:3.500A)
      removed outlier: 5.539A  pdb=" N   TYR C  70 " --> pdb=" O   ARG C 101 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   ARG C 101 " --> pdb=" O   TYR C  70 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   SER C  72 " --> pdb=" O   LYS C  99 " (cutoff:3.500A)
      removed outlier: 5.779A  pdb=" N   ALA C  94 " --> pdb=" O   GLU C 126 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   GLU C 126 " --> pdb=" O   ALA C  94 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LEU C  96 " --> pdb=" O   MET C 124 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 144 through 145
    Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454
    Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 158
    Processing sheet with id=AB7, first strand: chain 'C' and resid 285 through 286
    Processing sheet with id=AB8, first strand: chain 'C' and resid 255 through 257
      removed outlier: 7.081A  pdb=" N   ILE C 255 " --> pdb=" O   TYR C 262 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 296 through 297
      removed outlier: 4.638A  pdb=" N   MET C 315 " --> pdb=" O   VAL C 297 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581
      removed outlier: 5.995A  pdb=" N   GLU C 602 " --> pdb=" O   LYS C 593 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   THR C 595 " --> pdb=" O   THR C 600 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   THR C 600 " --> pdb=" O   THR C 595 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581
    Processing sheet with id=AC3, first strand: chain 'C' and resid 634 through 636
    Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717
      removed outlier: 6.445A  pdb=" N   ALA C 716 " --> pdb=" O   LEU C 783 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   MET C 768 " --> pdb=" O   ASP C 785 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'C' and resid 723 through 727
      removed outlier: 6.644A  pdb=" N   VAL C 733 " --> pdb=" O   GLN C 725 " (cutoff:3.500A)
      removed outlier: 4.746A  pdb=" N   VAL C 727 " --> pdb=" O   ARG C 731 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ARG C 731 " --> pdb=" O   VAL C 727 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 758
    Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 790
    Processing sheet with id=AC8, first strand: chain 'C' and resid 1209 through 1210
      removed outlier: 7.376A  pdb=" N   ILE C 816 " --> pdb=" O   LYS C1078 " (cutoff:3.500A)
      removed outlier: 7.937A  pdb=" N   ASN C1080 " --> pdb=" O   ILE C 816 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   VAL C 818 " --> pdb=" O   ASN C1080 " (cutoff:3.500A)
      removed outlier: 8.396A  pdb=" N   ILE C1096 " --> pdb=" O   ASN C 799 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   ARG C 801 " --> pdb=" O   ILE C1096 " (cutoff:3.500A)
      removed outlier: 7.494A  pdb=" N   LEU C1098 " --> pdb=" O   ARG C 801 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ALA C 803 " --> pdb=" O   LEU C1098 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   THR C1226 " --> pdb=" O   PHE C 804 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'C' and resid 830 through 841
      removed outlier: 6.319A  pdb=" N   LYS C1051 " --> pdb=" O   VAL C 931 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   VAL C 931 " --> pdb=" O   LYS C1051 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   TYR C1053 " --> pdb=" O   ILE C 929 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'C' and resid 830 through 841
    Processing sheet with id=AD2, first strand: chain 'C' and resid 849 through 850
    Processing sheet with id=AD3, first strand: chain 'C' and resid 882 through 884
      removed outlier: 6.723A  pdb=" N   LEU C 918 " --> pdb=" O   LEU C 883 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246
    Processing sheet with id=AD5, first strand: chain 'C' and resid 1335 through 1338
    Processing sheet with id=AD6, first strand: chain 'D' and resid 104 through 111
      removed outlier: 8.651A  pdb=" N   THR D 240 " --> pdb=" O   LEU D 107 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'D' and resid 145 through 147
      removed outlier: 4.134A  pdb=" N   ASP D 177 " --> pdb=" O   ILE D 147 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'D' and resid 253 through 254
    Processing sheet with id=AD9, first strand: chain 'D' and resid 526 through 527
    Processing sheet with id=AE1, first strand: chain 'D' and resid 809 through 811
    Processing sheet with id=AE2, first strand: chain 'D' and resid 820 through 822
    Processing sheet with id=AE3, first strand: chain 'D' and resid 825 through 827
      removed outlier: 7.070A  pdb=" N   GLU D 827 " --> pdb=" O   VAL D 831 " (cutoff:3.500A)
      removed outlier: 5.573A  pdb=" N   VAL D 831 " --> pdb=" O   GLU D 827 " (cutoff:3.500A)
    Processing sheet with id=AE4, first strand: chain 'D' and resid 848 through 849
      removed outlier: 7.017A  pdb=" N   VAL D 848 " --> pdb=" O   LEU D 857 " (cutoff:3.500A)
    Processing sheet with id=AE5, first strand: chain 'D' and resid 957 through 961
    Processing sheet with id=AE6, first strand: chain 'D' and resid 966 through 967
      removed outlier: 5.056A  pdb=" N   LEU D 973 " --> pdb=" O   LEU D1003 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LEU D1003 " --> pdb=" O   LEU D 973 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ALA D1001 " --> pdb=" O   ILE D 975 " (cutoff:3.500A)
    Processing sheet with id=AE7, first strand: chain 'D' and resid 1059 through 1062
      removed outlier: 3.863A  pdb=" N   LEU D1059 " --> pdb=" O   VAL D1107 " (cutoff:3.500A)
      removed outlier: 7.768A  pdb=" N   ALA D1105 " --> pdb=" O   VAL D1061 " (cutoff:3.500A)
    Processing sheet with id=AE8, first strand: chain 'D' and resid 1277 through 1278
    Processing sheet with id=AE9, first strand: chain 'M' and resid 277 through 278
      removed outlier: 7.148A  pdb=" N   LEU M 277 " --> pdb=" O   HIS M 391 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AE9

    1151 hydrogen bonds defined for protein.
    3225 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      103 hydrogen bonds
      202 hydrogen bond angles
      0 basepair planarities
      40 basepair parallelities
      81 stacking parallelities
  Total time for adding SS restraints: 14.57

  Time building geometry restraints manager: 12.02 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 8931
        1.33 -     1.46: 4565
        1.46 -     1.58: 15433
        1.58 -     1.70: 202
        1.70 -     1.82: 170
  Bond restraints: 29301
  Sorted by residual:
  bond pdb=" CG  PRO M 258 "
       pdb=" CD  PRO M 258 "
    ideal  model  delta    sigma   weight residual
    1.503  1.304  0.199 3.40e-02 8.65e+02 3.42e+01
  bond pdb=" N   PRO M 258 "
       pdb=" CA  PRO M 258 "
    ideal  model  delta    sigma   weight residual
    1.469  1.429  0.039 1.28e-02 6.10e+03 9.39e+00
  bond pdb=" CG  PRO D1139 "
       pdb=" CD  PRO D1139 "
    ideal  model  delta    sigma   weight residual
    1.503  1.401  0.102 3.40e-02 8.65e+02 8.93e+00
  bond pdb=" N   PRO M 258 "
       pdb=" CD  PRO M 258 "
    ideal  model  delta    sigma   weight residual
    1.473  1.513 -0.040 1.40e-02 5.10e+03 8.18e+00
  bond pdb=" CB  PRO M 258 "
       pdb=" CG  PRO M 258 "
    ideal  model  delta    sigma   weight residual
    1.492  1.618 -0.126 5.00e-02 4.00e+02 6.35e+00
  ... (remaining 29296 not shown)

  Histogram of bond angle deviations from ideal:
       88.97 -    97.98: 4
       97.98 -   107.00: 1347
      107.00 -   116.02: 18816
      116.02 -   125.04: 19473
      125.04 -   134.06: 610
  Bond angle restraints: 40250
  Sorted by residual:
  angle pdb=" CA  PRO M 258 "
        pdb=" N   PRO M 258 "
        pdb=" CD  PRO M 258 "
      ideal   model   delta    sigma   weight residual
     112.00   94.43   17.57 1.40e+00 5.10e-01 1.58e+02
  angle pdb=" N   PRO M 258 "
        pdb=" CD  PRO M 258 "
        pdb=" CG  PRO M 258 "
      ideal   model   delta    sigma   weight residual
     103.20   88.97   14.23 1.50e+00 4.44e-01 9.01e+01
  angle pdb=" CA  PRO D1139 "
        pdb=" N   PRO D1139 "
        pdb=" CD  PRO D1139 "
      ideal   model   delta    sigma   weight residual
     112.00  101.82   10.18 1.40e+00 5.10e-01 5.28e+01
  angle pdb=" N   ILE A 159 "
        pdb=" CA  ILE A 159 "
        pdb=" C   ILE A 159 "
      ideal   model   delta    sigma   weight residual
     113.53  107.94    5.59 9.80e-01 1.04e+00 3.25e+01
  angle pdb=" C   ASP D  67 "
        pdb=" CA  ASP D  67 "
        pdb=" CB  ASP D  67 "
      ideal   model   delta    sigma   weight residual
     116.54  110.16    6.38 1.15e+00 7.56e-01 3.07e+01
  ... (remaining 40245 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.34: 16635
       34.34 -    68.68: 918
       68.68 -   103.02: 42
      103.02 -   137.36: 2
      137.36 -   171.70: 2
  Dihedral angle restraints: 17599
    sinusoidal: 7140
      harmonic: 10459
  Sorted by residual:
  dihedral pdb=" CA  LEU D1138 "
           pdb=" C   LEU D1138 "
           pdb=" N   PRO D1139 "
           pdb=" CA  PRO D1139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  141.02   38.98     0      5.00e+00 4.00e-02 6.08e+01
  dihedral pdb=" CA  PHE C  15 "
           pdb=" C   PHE C  15 "
           pdb=" N   GLY C  16 "
           pdb=" CA  GLY C  16 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.59   22.41     0      5.00e+00 4.00e-02 2.01e+01
  dihedral pdb=" CA  PHE D 338 "
           pdb=" C   PHE D 338 "
           pdb=" N   ARG D 339 "
           pdb=" CA  ARG D 339 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.78  -21.22     0      5.00e+00 4.00e-02 1.80e+01
  ... (remaining 17596 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 3787
       0.050 -    0.100: 797
       0.100 -    0.150: 188
       0.150 -    0.200: 15
       0.200 -    0.250: 1
  Chirality restraints: 4788
  Sorted by residual:
  chirality pdb=" CB  ILE D 159 "
            pdb=" CA  ILE D 159 "
            pdb=" CG1 ILE D 159 "
            pdb=" CG2 ILE D 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.90   -0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CG  LEU D 324 "
            pdb=" CB  LEU D 324 "
            pdb=" CD1 LEU D 324 "
            pdb=" CD2 LEU D 324 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 9.55e-01
  chirality pdb=" CB  ILE M 144 "
            pdb=" CA  ILE M 144 "
            pdb=" CG1 ILE M 144 "
            pdb=" CG2 ILE M 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 8.06e-01
  ... (remaining 4785 not shown)

  Planarity restraints: 4929
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D1138 "    0.131 5.00e-02 4.00e+02   1.90e-01 5.80e+01
        pdb=" N   PRO D1139 "   -0.329 5.00e-02 4.00e+02
        pdb=" CA  PRO D1139 "    0.109 5.00e-02 4.00e+02
        pdb=" CD  PRO D1139 "    0.089 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP M 257 "    0.100 5.00e-02 4.00e+02   1.36e-01 2.95e+01
        pdb=" N   PRO M 258 "   -0.234 5.00e-02 4.00e+02
        pdb=" CA  PRO M 258 "    0.066 5.00e-02 4.00e+02
        pdb=" CD  PRO M 258 "    0.068 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE M 273 "   -0.069 5.00e-02 4.00e+02   1.02e-01 1.68e+01
        pdb=" N   PRO M 274 "    0.177 5.00e-02 4.00e+02
        pdb=" CA  PRO M 274 "   -0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO M 274 "   -0.056 5.00e-02 4.00e+02
  ... (remaining 4926 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.58: 228
        2.58 -     3.16: 24131
        3.16 -     3.74: 44604
        3.74 -     4.32: 58615
        4.32 -     4.90: 97701
  Nonbonded interactions: 225279
  Sorted by model distance:
  nonbonded pdb=" O3'   G R   4 "
            pdb="MG    MG D1501 "
     model   vdw
     2.006 2.170
  nonbonded pdb=" OD1 ASP D 460 "
            pdb="MG    MG D1501 "
     model   vdw
     2.037 2.170
  nonbonded pdb=" OD1 ASP D 464 "
            pdb="MG    MG D1501 "
     model   vdw
     2.091 2.170
  nonbonded pdb=" OG  SER D 326 "
            pdb=" OD1 ASP D 329 "
     model   vdw
     2.141 2.440
  nonbonded pdb=" NH1 ARG D 799 "
            pdb=" OE2 GLU D1146 "
     model   vdw
     2.153 2.520
  ... (remaining 225274 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.470
  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:          3.450
  Check model and map are aligned:         0.440
  Set scattering table:                    0.240
  Process input model:                     87.640
  Find NCS groups from input model:        1.180
  Set up NCS constraints:                  0.100
  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:             0.000
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   96.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3518
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      :  0.005   0.199  29301  Z= 0.324
  Angle     :  0.711  17.573  40250  Z= 0.386
  Chirality :  0.043   0.250   4788
  Planarity :  0.006   0.190   4929
  Dihedral  : 19.202 171.697  10851
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  6.67 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  : 29.98 %
    Favored  : 69.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.67 %
    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: -0.58 (0.14), residues: 3612
  helix:  0.95 (0.15), residues: 1276
  sheet:  0.46 (0.27), residues: 396
  loop : -1.55 (0.14), residues: 1940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP C 183 
 HIS   0.005   0.001   HIS D 113 
 PHE   0.015   0.002   PHE M 355 
 TYR   0.036   0.002   TYR C1053 
 ARG   0.008   0.001   ARG M 184 

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

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

  7224 Ramachandran restraints generated.
    3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7224 Ramachandran restraints generated.
    3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  770 residues out of total 3113 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 760
  time to evaluate  : 3.047 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 PHE cc_start: 0.4880 (m-80) cc_final: 0.4605 (m-10)
REVERT: A  223 ILE cc_start: 0.5677 (mt) cc_final: 0.5458 (mt)
REVERT: B  236 ASP cc_start: 0.5041 (t0) cc_final: 0.4717 (t0)
REVERT: C  189 ASP cc_start: 0.4148 (t70) cc_final: 0.3929 (t0)
REVERT: C  726 TYR cc_start: 0.3265 (t80) cc_final: 0.2905 (t80)
REVERT: D 1040 MET cc_start: 0.2818 (tpt) cc_final: 0.2010 (tpt)
REVERT: D 1357 ILE cc_start: 0.1264 (pt) cc_final: 0.0823 (pt)
REVERT: E   54 ILE cc_start: 0.3741 (mt) cc_final: 0.3363 (mt)
REVERT: M  270 GLU cc_start: 0.5301 (tp30) cc_final: 0.4568 (tm-30)
REVERT: M  365 MET cc_start: 0.0162 (pmm) cc_final: -0.1949 (ppp)
  outliers start: 10
  outliers final: 0
  residues processed: 767
  average time/residue: 0.4440
  time to fit residues: 515.7865
Evaluate side-chains
  468 residues out of total 3113 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 468
  time to evaluate  : 2.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 371
   random chunks:
   chunk 313 optimal weight:    9.9990
   chunk 281 optimal weight:    2.9990
   chunk 156 optimal weight:    0.9990
   chunk 96 optimal weight:    0.0170
   chunk 189 optimal weight:    0.8980
   chunk 150 optimal weight:    0.9990
   chunk 290 optimal weight:    4.9990
   chunk 112 optimal weight:    5.9990
   chunk 176 optimal weight:    9.9990
   chunk 216 optimal weight:    0.0970
   chunk 336 optimal weight:    9.9990
   overall best weight:    0.6020

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

Flipped N/Q/H residues before XYZ refinement:
A  23 HIS
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  36 GLN
C 314 ASN
** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 658 GLN
** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 762 ASN
C1108 ASN
C1111 GLN
** C1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1244 HIS
** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 186 GLN
D 266 ASN
** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 594 GLN
D 665 GLN
D1238 GLN
D1249 ASN
** D1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1350 ASN
M 121 GLN
** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4018
moved from start:          0.2909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  29301  Z= 0.211
  Angle     :  0.703  11.444  40250  Z= 0.355
  Chirality :  0.044   0.196   4788
  Planarity :  0.005   0.126   4929
  Dihedral  : 16.271 171.910   5044
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 16.10
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  5.76 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 29.91 %
    Favored  : 65.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.67 %
    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: -0.53 (0.14), residues: 3612
  helix:  0.87 (0.15), residues: 1333
  sheet:  0.52 (0.27), residues: 385
  loop : -1.49 (0.14), residues: 1894

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 183 
 HIS   0.017   0.002   HIS D  80 
 PHE   0.025   0.002   PHE M 355 
 TYR   0.032   0.002   TYR D 349 
 ARG   0.011   0.001   ARG D 133 

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

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

  7224 Ramachandran restraints generated.
    3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7224 Ramachandran restraints generated.
    3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  625 residues out of total 3113 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 123
    poor density    : 502
  time to evaluate  : 2.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 THR cc_start: 0.2946 (OUTLIER) cc_final: 0.1561 (p)
REVERT: A  316 MET cc_start: 0.4744 (ppp) cc_final: 0.4491 (ppp)
REVERT: C   47 TYR cc_start: 0.2789 (OUTLIER) cc_final: 0.2348 (p90)
REVERT: C  900 LYS cc_start: 0.5208 (OUTLIER) cc_final: 0.4595 (mttt)
REVERT: C 1022 LYS cc_start: 0.7890 (mttp) cc_final: 0.7555 (mmmt)
REVERT: D   43 THR cc_start: 0.2773 (OUTLIER) cc_final: 0.2562 (m)
REVERT: D 1040 MET cc_start: 0.2669 (tpt) cc_final: 0.2035 (tpt)
REVERT: M  270 GLU cc_start: 0.5462 (tp30) cc_final: 0.4657 (tm-30)
REVERT: M  363 LYS cc_start: 0.4223 (mmmt) cc_final: 0.3930 (mmmt)
REVERT: M  365 MET cc_start: 0.0603 (pmm) cc_final: -0.1409 (ppp)
  outliers start: 123
  outliers final: 45
  residues processed: 596
  average time/residue: 0.4138
  time to fit residues: 386.5590
Evaluate side-chains
  462 residues out of total 3113 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 49
    poor density    : 413
  time to evaluate  : 3.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   71 LYS
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  174 ASP
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  114 ASP
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain C residue   47 TYR
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  530 ILE
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain C residue  589 THR
Chi-restraints excluded: chain C residue  635 THR
Chi-restraints excluded: chain C residue  735 LYS
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  793 GLU
Chi-restraints excluded: chain C residue  819 SER
Chi-restraints excluded: chain C residue  831 ILE
Chi-restraints excluded: chain C residue  833 ILE
Chi-restraints excluded: chain C residue  900 LYS
Chi-restraints excluded: chain C residue  930 ASP
Chi-restraints excluded: chain C residue  933 VAL
Chi-restraints excluded: chain C residue 1154 ASP
Chi-restraints excluded: chain C residue 1176 LEU
Chi-restraints excluded: chain C residue 1201 LEU
Chi-restraints excluded: chain C residue 1293 VAL
Chi-restraints excluded: chain C residue 1302 THR
Chi-restraints excluded: chain D residue   20 ILE
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue   70 CYS
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  177 ASP
Chi-restraints excluded: chain D residue  408 VAL
Chi-restraints excluded: chain D residue  423 LEU
Chi-restraints excluded: chain D residue  473 THR
Chi-restraints excluded: chain D residue  484 MET
Chi-restraints excluded: chain D residue  590 SER
Chi-restraints excluded: chain D residue  619 ILE
Chi-restraints excluded: chain D residue  721 SER
Chi-restraints excluded: chain D residue  820 ILE
Chi-restraints excluded: chain D residue  869 CYS
Chi-restraints excluded: chain D residue  928 THR
Chi-restraints excluded: chain D residue 1351 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 371
   random chunks:
   chunk 187 optimal weight:    0.0980
   chunk 104 optimal weight:    2.9990
   chunk 280 optimal weight:    8.9990
   chunk 229 optimal weight:    9.9990
   chunk 92 optimal weight:   20.0000
   chunk 337 optimal weight:   20.0000
   chunk 364 optimal weight:   50.0000
   chunk 300 optimal weight:    0.3980
   chunk 334 optimal weight:    1.9990
   chunk 115 optimal weight:    6.9990
   chunk 270 optimal weight:    1.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 658 GLN
C 659 GLN
C 686 GLN
C 725 GLN
C 762 ASN
C 932 GLN
C1108 ASN
** C1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1244 HIS
C1257 GLN
D 309 ASN
D 364 HIS
D 365 GLN
** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1218 HIS
D1249 ASN
** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4532
moved from start:          0.4355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  29301  Z= 0.214
  Angle     :  0.693  11.082  40250  Z= 0.349
  Chirality :  0.044   0.230   4788
  Planarity :  0.005   0.105   4929
  Dihedral  : 16.155 170.729   5044
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 15.70
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.73 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 29.87 %
    Favored  : 65.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.67 %
    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: -0.55 (0.14), residues: 3612
  helix:  0.79 (0.14), residues: 1342
  sheet:  0.60 (0.26), residues: 373
  loop : -1.48 (0.14), residues: 1897

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.003   TRP D 580 
 HIS   0.013   0.002   HIS D  80 
 PHE   0.026   0.002   PHE C 629 
 TYR   0.032   0.002   TYR D 589 
 ARG   0.009   0.001   ARG D 744 

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

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

  7224 Ramachandran restraints generated.
    3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7224 Ramachandran restraints generated.
    3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  602 residues out of total 3113 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 129
    poor density    : 473
  time to evaluate  : 3.061 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.3875 (OUTLIER) cc_final: 0.3652 (t70)
REVERT: C   47 TYR cc_start: 0.3596 (OUTLIER) cc_final: 0.2937 (p90)
REVERT: C   68 LEU cc_start: 0.6848 (tp) cc_final: 0.6297 (tt)
REVERT: C  409 LEU cc_start: 0.5281 (OUTLIER) cc_final: 0.4895 (tp)
REVERT: C  430 LYS cc_start: 0.3158 (mmtt) cc_final: 0.2861 (mmtt)
REVERT: C  900 LYS cc_start: 0.5539 (OUTLIER) cc_final: 0.4781 (mttt)
REVERT: C 1022 LYS cc_start: 0.7896 (mttp) cc_final: 0.7655 (mmmt)
REVERT: D  894 VAL cc_start: 0.4728 (OUTLIER) cc_final: 0.4406 (t)
REVERT: D 1040 MET cc_start: 0.2656 (tpt) cc_final: 0.2157 (tpt)
REVERT: M  270 GLU cc_start: 0.5667 (tp30) cc_final: 0.5399 (tp30)
REVERT: M  363 LYS cc_start: 0.4345 (mmmt) cc_final: 0.4132 (mmmt)
REVERT: M  365 MET cc_start: 0.0187 (pmm) cc_final: -0.1908 (ppp)
  outliers start: 129
  outliers final: 55
  residues processed: 566
  average time/residue: 0.3860
  time to fit residues: 349.6867
Evaluate side-chains
  467 residues out of total 3113 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 60
    poor density    : 407
  time to evaluate  : 3.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  231 PHE
Chi-restraints excluded: chain B residue   26 VAL
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  114 ASP
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  183 ILE
Chi-restraints excluded: chain B residue  229 GLU
Chi-restraints excluded: chain C residue   30 ILE
Chi-restraints excluded: chain C residue   46 GLN
Chi-restraints excluded: chain C residue   47 TYR
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  409 LEU
Chi-restraints excluded: chain C residue  492 MET
Chi-restraints excluded: chain C residue  494 ASN
Chi-restraints excluded: chain C residue  530 ILE
Chi-restraints excluded: chain C residue  589 THR
Chi-restraints excluded: chain C residue  655 VAL
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  831 ILE
Chi-restraints excluded: chain C residue  900 LYS
Chi-restraints excluded: chain C residue  933 VAL
Chi-restraints excluded: chain C residue  960 LEU
Chi-restraints excluded: chain C residue 1018 TYR
Chi-restraints excluded: chain C residue 1115 THR
Chi-restraints excluded: chain C residue 1154 ASP
Chi-restraints excluded: chain C residue 1157 GLN
Chi-restraints excluded: chain D residue   20 ILE
Chi-restraints excluded: chain D residue   61 ILE
Chi-restraints excluded: chain D residue   70 CYS
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  223 LEU
Chi-restraints excluded: chain D residue  309 ASN
Chi-restraints excluded: chain D residue  355 ILE
Chi-restraints excluded: chain D residue  408 VAL
Chi-restraints excluded: chain D residue  473 THR
Chi-restraints excluded: chain D residue  518 VAL
Chi-restraints excluded: chain D residue  624 ILE
Chi-restraints excluded: chain D residue  635 SER
Chi-restraints excluded: chain D residue  760 THR
Chi-restraints excluded: chain D residue  772 TYR
Chi-restraints excluded: chain D residue  820 ILE
Chi-restraints excluded: chain D residue  869 CYS
Chi-restraints excluded: chain D residue  894 VAL
Chi-restraints excluded: chain D residue  928 THR
Chi-restraints excluded: chain D residue 1226 VAL
Chi-restraints excluded: chain D residue 1249 ASN
Chi-restraints excluded: chain D residue 1253 ILE
Chi-restraints excluded: chain D residue 1292 LEU
Chi-restraints excluded: chain D residue 1344 LEU
Chi-restraints excluded: chain D residue 1351 VAL
Chi-restraints excluded: chain E residue    4 VAL
Chi-restraints excluded: chain E residue   61 ASN
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain M residue  210 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 371
   random chunks:
   chunk 333 optimal weight:    5.9990
   chunk 253 optimal weight:    0.0970
   chunk 175 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 161 optimal weight:    8.9990
   chunk 226 optimal weight:    7.9990
   chunk 338 optimal weight:   20.0000
   chunk 358 optimal weight:   20.0000
   chunk 176 optimal weight:    3.9990
   chunk 321 optimal weight:    5.9990
   chunk 96 optimal weight:    5.9990
   overall best weight:    4.4186

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 186 ASN
B  75 GLN
B  93 GLN
C 314 ASN
** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1108 ASN
** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C1257 GLN
** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 309 ASN
D 430 HIS
** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 265 GLN
** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6401
moved from start:          0.9295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.187  29301  Z= 0.459
  Angle     :  0.973  20.387  40250  Z= 0.506
  Chirality :  0.055   0.629   4788
  Planarity :  0.008   0.150   4929
  Dihedral  : 16.591 167.024   5044
  Min Nonbonded Distance : 1.891

Molprobity Statistics.
  All-atom Clashscore : 23.62
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.89 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  7.48 %
    Allowed  : 27.72 %
    Favored  : 64.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.67 %
    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: -1.29 (0.13), residues: 3612
  helix:  0.00 (0.14), residues: 1346
  sheet: -0.03 (0.27), residues: 381
  loop : -1.71 (0.13), residues: 1885

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.005   TRP D 580 
 HIS   0.018   0.003   HIS D1252 
 PHE   0.035   0.004   PHE C  53 
 TYR   0.041   0.004   TYR D 589 
 ARG   0.022   0.001   ARG D 250 

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

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

  7224 Ramachandran restraints generated.
    3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7224 Ramachandran restraints generated.
    3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  681 residues out of total 3113 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 195
    poor density    : 486
  time to evaluate  : 3.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 PHE cc_start: 0.6521 (m-10) cc_final: 0.6264 (m-80)
REVERT: A   57 THR cc_start: 0.6948 (p) cc_final: 0.6380 (m)
REVERT: A  142 MET cc_start: 0.6571 (ppp) cc_final: 0.5981 (ppp)
REVERT: B   37 HIS cc_start: 0.8126 (OUTLIER) cc_final: 0.7210 (t-90)
REVERT: C 1022 LYS cc_start: 0.7877 (mttp) cc_final: 0.7607 (mmmt)
REVERT: C 1108 ASN cc_start: 0.7284 (OUTLIER) cc_final: 0.7060 (p0)
REVERT: D 1040 MET cc_start: 0.2774 (tpt) cc_final: 0.1973 (tpt)
REVERT: D 1287 ILE cc_start: 0.4900 (OUTLIER) cc_final: 0.4557 (mt)
REVERT: M  270 GLU cc_start: 0.6448 (tp30) cc_final: 0.5866 (tp30)
REVERT: M  455 ARG cc_start: 0.5010 (tpt90) cc_final: 0.2558 (tmm160)
  outliers start: 195
  outliers final: 77
  residues processed: 639
  average time/residue: 0.3813
  time to fit residues: 391.9433
Evaluate side-chains
  446 residues out of total 3113 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 80
    poor density    : 366
  time to evaluate  : 3.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  207 THR
Chi-restraints excluded: chain B residue   16 ILE
Chi-restraints excluded: chain B residue   26 VAL
Chi-restraints excluded: chain B residue   37 HIS
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  150 HIS
Chi-restraints excluded: chain C residue  177 ILE
Chi-restraints excluded: chain C residue  185 ASP
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  484 LEU
Chi-restraints excluded: chain C residue  493 ILE
Chi-restraints excluded: chain C residue  499 SER
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain C residue  719 LYS
Chi-restraints excluded: chain C residue  785 ASP
Chi-restraints excluded: chain C residue  838 CYS
Chi-restraints excluded: chain C residue  840 SER
Chi-restraints excluded: chain C residue  871 VAL
Chi-restraints excluded: chain C residue  927 THR
Chi-restraints excluded: chain C residue 1018 TYR
Chi-restraints excluded: chain C residue 1082 ILE
Chi-restraints excluded: chain C residue 1108 ASN
Chi-restraints excluded: chain C residue 1112 ILE
Chi-restraints excluded: chain C residue 1115 THR
Chi-restraints excluded: chain C residue 1154 ASP
Chi-restraints excluded: chain C residue 1157 GLN
Chi-restraints excluded: chain C residue 1227 VAL
Chi-restraints excluded: chain C residue 1234 LYS
Chi-restraints excluded: chain C residue 1293 VAL
Chi-restraints excluded: chain C residue 1295 SER
Chi-restraints excluded: chain C residue 1337 ILE
Chi-restraints excluded: chain D residue   61 ILE
Chi-restraints excluded: chain D residue   70 CYS
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue  223 LEU
Chi-restraints excluded: chain D residue  239 LEU
Chi-restraints excluded: chain D residue  329 ASP
Chi-restraints excluded: chain D residue  350 SER
Chi-restraints excluded: chain D residue  434 ILE
Chi-restraints excluded: chain D residue  449 LEU
Chi-restraints excluded: chain D residue  474 LEU
Chi-restraints excluded: chain D residue  514 THR
Chi-restraints excluded: chain D residue  518 VAL
Chi-restraints excluded: chain D residue  564 VAL
Chi-restraints excluded: chain D residue  708 ASN
Chi-restraints excluded: chain D residue  721 SER
Chi-restraints excluded: chain D residue  760 THR
Chi-restraints excluded: chain D residue  765 GLU
Chi-restraints excluded: chain D residue  767 LEU
Chi-restraints excluded: chain D residue  811 GLU
Chi-restraints excluded: chain D residue  840 LEU
Chi-restraints excluded: chain D residue  858 VAL
Chi-restraints excluded: chain D residue  915 ILE
Chi-restraints excluded: chain D residue  928 THR
Chi-restraints excluded: chain D residue 1169 THR
Chi-restraints excluded: chain D residue 1226 VAL
Chi-restraints excluded: chain D residue 1230 THR
Chi-restraints excluded: chain D residue 1253 ILE
Chi-restraints excluded: chain D residue 1287 ILE
Chi-restraints excluded: chain D residue 1292 LEU
Chi-restraints excluded: chain D residue 1344 LEU
Chi-restraints excluded: chain E residue   19 LEU
Chi-restraints excluded: chain E residue   61 ASN
Chi-restraints excluded: chain M residue  155 THR
Chi-restraints excluded: chain M residue  201 ILE
Chi-restraints excluded: chain M residue  210 THR
Chi-restraints excluded: chain M residue  355 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 371
   random chunks:
   chunk 298 optimal weight:    0.1980
   chunk 203 optimal weight:    8.9990
   chunk 5 optimal weight:   10.0000
   chunk 267 optimal weight:    5.9990
   chunk 147 optimal weight:    0.9980
   chunk 306 optimal weight:    0.6980
   chunk 247 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   chunk 183 optimal weight:    8.9990
   chunk 321 optimal weight:    9.9990
   chunk 90 optimal weight:    0.0980
   overall best weight:    1.5982

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

Flipped N/Q/H residues before XYZ refinement:
** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 314 ASN
** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 737 ASN
** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1070 HIS
C1108 ASN
** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1257 GLN
D 276 ASN
D 469 HIS
** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 921 GLN
** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1366 HIS
** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6447
moved from start:          0.9776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  29301  Z= 0.210
  Angle     :  0.702  14.848  40250  Z= 0.351
  Chirality :  0.043   0.197   4788
  Planarity :  0.005   0.066   4929
  Dihedral  : 16.335 169.023   5044
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 18.21
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.51 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 32.98 %
    Favored  : 63.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.34 %
    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: -0.82 (0.14), residues: 3612
  helix:  0.59 (0.14), residues: 1333
  sheet:  0.23 (0.27), residues: 371
  loop : -1.57 (0.13), residues: 1908

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP D 580 
 HIS   0.009   0.001   HIS D  80 
 PHE   0.022   0.002   PHE D 892 
 TYR   0.028   0.002   TYR D 555 
 ARG   0.010   0.001   ARG C 454 

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

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

  7224 Ramachandran restraints generated.
    3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7224 Ramachandran restraints generated.
    3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  503 residues out of total 3113 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 101
    poor density    : 402
  time to evaluate  : 3.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 MET cc_start: 0.6840 (ppp) cc_final: 0.6310 (ppp)
REVERT: C  900 LYS cc_start: 0.5647 (OUTLIER) cc_final: 0.5060 (mttt)
REVERT: D  772 TYR cc_start: 0.6397 (OUTLIER) cc_final: 0.5834 (m-80)
REVERT: D 1040 MET cc_start: 0.2385 (tpt) cc_final: 0.1552 (tpt)
REVERT: M  270 GLU cc_start: 0.6503 (tp30) cc_final: 0.6011 (tp30)
REVERT: M  455 ARG cc_start: 0.4941 (tpt90) cc_final: 0.2529 (tmm160)
  outliers start: 101
  outliers final: 51
  residues processed: 485
  average time/residue: 0.3795
  time to fit residues: 296.1224
Evaluate side-chains
  410 residues out of total 3113 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 53
    poor density    : 357
  time to evaluate  : 2.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  137 ASN
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain B residue   26 VAL
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  185 ASP
Chi-restraints excluded: chain C residue  484 LEU
Chi-restraints excluded: chain C residue  530 ILE
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain C residue  651 ASP
Chi-restraints excluded: chain C residue  719 LYS
Chi-restraints excluded: chain C residue  838 CYS
Chi-restraints excluded: chain C residue  900 LYS
Chi-restraints excluded: chain C residue 1049 ILE
Chi-restraints excluded: chain C residue 1052 VAL
Chi-restraints excluded: chain C residue 1112 ILE
Chi-restraints excluded: chain C residue 1115 THR
Chi-restraints excluded: chain C residue 1154 ASP
Chi-restraints excluded: chain C residue 1275 VAL
Chi-restraints excluded: chain C residue 1309 VAL
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue   61 ILE
Chi-restraints excluded: chain D residue   65 VAL
Chi-restraints excluded: chain D residue   70 CYS
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  119 SER
Chi-restraints excluded: chain D residue  355 ILE
Chi-restraints excluded: chain D residue  387 LEU
Chi-restraints excluded: chain D residue  412 LEU
Chi-restraints excluded: chain D residue  415 VAL
Chi-restraints excluded: chain D residue  474 LEU
Chi-restraints excluded: chain D residue  478 LEU
Chi-restraints excluded: chain D residue  514 THR
Chi-restraints excluded: chain D residue  622 ASP
Chi-restraints excluded: chain D residue  624 ILE
Chi-restraints excluded: chain D residue  721 SER
Chi-restraints excluded: chain D residue  772 TYR
Chi-restraints excluded: chain D residue  858 VAL
Chi-restraints excluded: chain D residue  882 VAL
Chi-restraints excluded: chain D residue 1226 VAL
Chi-restraints excluded: chain D residue 1253 ILE
Chi-restraints excluded: chain E residue   47 THR
Chi-restraints excluded: chain M residue  190 VAL
Chi-restraints excluded: chain M residue  210 THR
Chi-restraints excluded: chain M residue  355 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 371
   random chunks:
   chunk 120 optimal weight:    2.9990
   chunk 322 optimal weight:    7.9990
   chunk 70 optimal weight:    6.9990
   chunk 210 optimal weight:   30.0000
   chunk 88 optimal weight:    0.0030
   chunk 358 optimal weight:    7.9990
   chunk 297 optimal weight:    0.9990
   chunk 166 optimal weight:    7.9990
   chunk 29 optimal weight:   10.0000
   chunk 118 optimal weight:   10.0000
   chunk 188 optimal weight:    8.9990
   overall best weight:    3.7998

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

Flipped N/Q/H residues before XYZ refinement:
** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 139 ASN
** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1116 HIS
** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1313 HIS
** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  62 GLN
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7004
moved from start:          1.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075  29301  Z= 0.324
  Angle     :  0.792  16.874  40250  Z= 0.404
  Chirality :  0.047   0.300   4788
  Planarity :  0.006   0.093   4929
  Dihedral  : 16.357 170.501   5044
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 19.61
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.92 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 32.02 %
    Favored  : 63.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.67 %
    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: -0.90 (0.14), residues: 3612
  helix:  0.45 (0.14), residues: 1330
  sheet:  0.09 (0.27), residues: 356
  loop : -1.53 (0.13), residues: 1926

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.004   TRP D 115 
 HIS   0.014   0.002   HIS D  80 
 PHE   0.029   0.003   PHE C 645 
 TYR   0.024   0.002   TYR C   3 
 ARG   0.028   0.001   ARG D 297 

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

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

  7224 Ramachandran restraints generated.
    3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7224 Ramachandran restraints generated.
    3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  490 residues out of total 3113 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 123
    poor density    : 367
  time to evaluate  : 3.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 MET cc_start: 0.7052 (ppp) cc_final: 0.6662 (ptt)
REVERT: B   37 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7463 (t-90)
REVERT: C   47 TYR cc_start: 0.6553 (OUTLIER) cc_final: 0.6226 (p90)
REVERT: C  430 LYS cc_start: 0.5770 (mmtt) cc_final: 0.5427 (mmtt)
REVERT: C  900 LYS cc_start: 0.6212 (OUTLIER) cc_final: 0.5519 (mttt)
REVERT: C 1274 GLU cc_start: 0.6949 (mp0) cc_final: 0.6620 (mp0)
REVERT: C 1290 MET cc_start: 0.7070 (mtt) cc_final: 0.6768 (mtt)
REVERT: D  772 TYR cc_start: 0.6764 (OUTLIER) cc_final: 0.6361 (m-80)
REVERT: D 1040 MET cc_start: 0.2235 (tpt) cc_final: 0.1331 (tpt)
REVERT: D 1344 LEU cc_start: 0.6642 (mm) cc_final: 0.6399 (mm)
REVERT: M  270 GLU cc_start: 0.6766 (tp30) cc_final: 0.6114 (tp30)
REVERT: M  455 ARG cc_start: 0.4698 (tpt90) cc_final: 0.2655 (tmm160)
  outliers start: 123
  outliers final: 62
  residues processed: 454
  average time/residue: 0.3726
  time to fit residues: 276.4874
Evaluate side-chains
  359 residues out of total 3113 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 66
    poor density    : 293
  time to evaluate  : 3.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain B residue   26 VAL
Chi-restraints excluded: chain B residue   37 HIS
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain C residue   47 TYR
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  177 ILE
Chi-restraints excluded: chain C residue  409 LEU
Chi-restraints excluded: chain C residue  432 LEU
Chi-restraints excluded: chain C residue  499 SER
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain C residue  719 LYS
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  802 VAL
Chi-restraints excluded: chain C residue  838 CYS
Chi-restraints excluded: chain C residue  900 LYS
Chi-restraints excluded: chain C residue  927 THR
Chi-restraints excluded: chain C residue  928 VAL
Chi-restraints excluded: chain C residue 1047 LEU
Chi-restraints excluded: chain C residue 1049 ILE
Chi-restraints excluded: chain C residue 1052 VAL
Chi-restraints excluded: chain C residue 1112 ILE
Chi-restraints excluded: chain C residue 1115 THR
Chi-restraints excluded: chain C residue 1154 ASP
Chi-restraints excluded: chain C residue 1295 SER
Chi-restraints excluded: chain D residue    7 PHE
Chi-restraints excluded: chain D residue   20 ILE
Chi-restraints excluded: chain D residue   61 ILE
Chi-restraints excluded: chain D residue   70 CYS
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  114 ILE
Chi-restraints excluded: chain D residue  239 LEU
Chi-restraints excluded: chain D residue  262 THR
Chi-restraints excluded: chain D residue  268 LEU
Chi-restraints excluded: chain D residue  338 PHE
Chi-restraints excluded: chain D residue  412 LEU
Chi-restraints excluded: chain D residue  415 VAL
Chi-restraints excluded: chain D residue  441 LEU
Chi-restraints excluded: chain D residue  449 LEU
Chi-restraints excluded: chain D residue  760 THR
Chi-restraints excluded: chain D residue  772 TYR
Chi-restraints excluded: chain D residue  858 VAL
Chi-restraints excluded: chain D residue  915 ILE
Chi-restraints excluded: chain D residue 1162 ILE
Chi-restraints excluded: chain D residue 1169 THR
Chi-restraints excluded: chain D residue 1177 ILE
Chi-restraints excluded: chain D residue 1226 VAL
Chi-restraints excluded: chain D residue 1230 THR
Chi-restraints excluded: chain D residue 1253 ILE
Chi-restraints excluded: chain D residue 1260 MET
Chi-restraints excluded: chain D residue 1273 ASP
Chi-restraints excluded: chain D residue 1320 ILE
Chi-restraints excluded: chain D residue 1329 THR
Chi-restraints excluded: chain E residue   19 LEU
Chi-restraints excluded: chain E residue   46 THR
Chi-restraints excluded: chain E residue   47 THR
Chi-restraints excluded: chain M residue  210 THR
Chi-restraints excluded: chain M residue  355 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 371
   random chunks:
   chunk 346 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 204 optimal weight:    7.9990
   chunk 262 optimal weight:    7.9990
   chunk 203 optimal weight:    2.9990
   chunk 302 optimal weight:   50.0000
   chunk 200 optimal weight:    1.9990
   chunk 357 optimal weight:   20.0000
   chunk 223 optimal weight:    2.9990
   chunk 218 optimal weight:    3.9990
   chunk 165 optimal weight:   20.0000
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  93 GLN
** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 266 ASN
** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 504 GLN
** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7143
moved from start:          1.2950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  29301  Z= 0.281
  Angle     :  0.736  17.211  40250  Z= 0.368
  Chirality :  0.045   0.321   4788
  Planarity :  0.005   0.090   4929
  Dihedral  : 16.318 169.654   5044
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 18.25
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.20 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 35.05 %
    Favored  : 61.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.67 %
    Twisted General : 0.03 %

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: -0.67 (0.14), residues: 3612
  helix:  0.67 (0.14), residues: 1327
  sheet:  0.16 (0.27), residues: 367
  loop : -1.42 (0.14), residues: 1918

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.063   0.003   TRP D 115 
 HIS   0.010   0.001   HIS D  80 
 PHE   0.021   0.002   PHE C 505 
 TYR   0.022   0.002   TYR A 152 
 ARG   0.012   0.001   ARG D1330 

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

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

  7224 Ramachandran restraints generated.
    3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7224 Ramachandran restraints generated.
    3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  398 residues out of total 3113 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 78
    poor density    : 320
  time to evaluate  : 3.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 MET cc_start: 0.7936 (mmm) cc_final: 0.7572 (mmt)
REVERT: C   47 TYR cc_start: 0.6538 (OUTLIER) cc_final: 0.6226 (p90)
REVERT: C  517 GLN cc_start: 0.7819 (tp40) cc_final: 0.7539 (tp40)
REVERT: C  742 TYR cc_start: 0.6916 (m-10) cc_final: 0.6301 (m-10)
REVERT: C  900 LYS cc_start: 0.6274 (OUTLIER) cc_final: 0.5476 (mttt)
REVERT: C 1023 HIS cc_start: 0.8216 (m90) cc_final: 0.7997 (m90)
REVERT: D  102 MET cc_start: 0.6150 (mmt) cc_final: 0.5926 (mmt)
REVERT: D  400 MET cc_start: 0.7015 (tmm) cc_final: 0.6718 (ttt)
REVERT: D  513 MET cc_start: 0.6958 (tpp) cc_final: 0.6546 (ttt)
REVERT: D  772 TYR cc_start: 0.6857 (OUTLIER) cc_final: 0.6320 (m-80)
REVERT: D 1040 MET cc_start: 0.2346 (tpt) cc_final: 0.1683 (tpt)
REVERT: D 1305 ASP cc_start: 0.5125 (m-30) cc_final: 0.4832 (m-30)
REVERT: M  154 LEU cc_start: 0.4935 (mt) cc_final: 0.4416 (mt)
REVERT: M  270 GLU cc_start: 0.6699 (tp30) cc_final: 0.6232 (tp30)
REVERT: M  455 ARG cc_start: 0.5293 (tpt90) cc_final: 0.3077 (tmm160)
  outliers start: 78
  outliers final: 46
  residues processed: 379
  average time/residue: 0.3833
  time to fit residues: 236.2104
Evaluate side-chains
  335 residues out of total 3113 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 49
    poor density    : 286
  time to evaluate  : 3.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ILE
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain B residue   26 VAL
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain C residue   47 TYR
Chi-restraints excluded: chain C residue   80 PHE
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  177 ILE
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain C residue  680 LEU
Chi-restraints excluded: chain C residue  838 CYS
Chi-restraints excluded: chain C residue  900 LYS
Chi-restraints excluded: chain C residue  928 VAL
Chi-restraints excluded: chain C residue 1049 ILE
Chi-restraints excluded: chain C residue 1052 VAL
Chi-restraints excluded: chain C residue 1115 THR
Chi-restraints excluded: chain C residue 1154 ASP
Chi-restraints excluded: chain D residue   61 ILE
Chi-restraints excluded: chain D residue   70 CYS
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  114 ILE
Chi-restraints excluded: chain D residue  239 LEU
Chi-restraints excluded: chain D residue  252 LEU
Chi-restraints excluded: chain D residue  262 THR
Chi-restraints excluded: chain D residue  265 LEU
Chi-restraints excluded: chain D residue  338 PHE
Chi-restraints excluded: chain D residue  350 SER
Chi-restraints excluded: chain D residue  408 VAL
Chi-restraints excluded: chain D residue  415 VAL
Chi-restraints excluded: chain D residue  504 GLN
Chi-restraints excluded: chain D residue  506 VAL
Chi-restraints excluded: chain D residue  674 THR
Chi-restraints excluded: chain D residue  772 TYR
Chi-restraints excluded: chain D residue  802 ASP
Chi-restraints excluded: chain D residue  858 VAL
Chi-restraints excluded: chain D residue  910 ASN
Chi-restraints excluded: chain D residue  915 ILE
Chi-restraints excluded: chain D residue  921 GLN
Chi-restraints excluded: chain D residue 1250 ASP
Chi-restraints excluded: chain D residue 1320 ILE
Chi-restraints excluded: chain E residue   11 GLU
Chi-restraints excluded: chain M residue  120 LEU
Chi-restraints excluded: chain M residue  155 THR
Chi-restraints excluded: chain M residue  210 THR
Chi-restraints excluded: chain M residue  355 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 371
   random chunks:
   chunk 221 optimal weight:    0.0980
   chunk 142 optimal weight:    0.9990
   chunk 213 optimal weight:   30.0000
   chunk 107 optimal weight:    4.9990
   chunk 70 optimal weight:    7.9990
   chunk 69 optimal weight:    6.9990
   chunk 227 optimal weight:    6.9990
   chunk 243 optimal weight:    0.8980
   chunk 176 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 281 optimal weight:    0.0170
   overall best weight:    0.6020

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

Flipped N/Q/H residues before XYZ refinement:
** A  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 128 HIS
** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1108 ASN
** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1116 HIS
** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7069
moved from start:          1.3073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  29301  Z= 0.193
  Angle     :  0.701  14.017  40250  Z= 0.347
  Chirality :  0.043   0.187   4788
  Planarity :  0.005   0.084   4929
  Dihedral  : 16.273 171.918   5044
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 16.43
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  6.04 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 34.55 %
    Favored  : 62.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.67 %
    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: -0.47 (0.14), residues: 3612
  helix:  0.94 (0.14), residues: 1316
  sheet:  0.31 (0.28), residues: 355
  loop : -1.36 (0.14), residues: 1941

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP D 236 
 HIS   0.009   0.001   HIS D  80 
 PHE   0.015   0.002   PHE C 390 
 TYR   0.028   0.002   TYR C  26 
 ARG   0.008   0.001   ARG M 196 

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

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

  7224 Ramachandran restraints generated.
    3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7224 Ramachandran restraints generated.
    3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  392 residues out of total 3113 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 66
    poor density    : 326
  time to evaluate  : 3.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 MET cc_start: 0.7818 (mmm) cc_final: 0.7503 (mmt)
REVERT: B   51 MET cc_start: 0.7089 (tpp) cc_final: 0.6853 (tpp)
REVERT: C   47 TYR cc_start: 0.6511 (OUTLIER) cc_final: 0.6235 (p90)
REVERT: C   80 PHE cc_start: 0.7477 (OUTLIER) cc_final: 0.6764 (m-80)
REVERT: C  517 GLN cc_start: 0.7681 (tp40) cc_final: 0.7145 (tp-100)
REVERT: C  523 GLU cc_start: 0.5606 (mt-10) cc_final: 0.5324 (mt-10)
REVERT: C  741 MET cc_start: 0.7554 (mmt) cc_final: 0.7177 (mmm)
REVERT: C  900 LYS cc_start: 0.6391 (OUTLIER) cc_final: 0.5604 (mttt)
REVERT: C 1023 HIS cc_start: 0.8150 (m90) cc_final: 0.7866 (m90)
REVERT: D  400 MET cc_start: 0.6965 (tmm) cc_final: 0.6658 (ttt)
REVERT: D  513 MET cc_start: 0.6880 (tpp) cc_final: 0.6430 (ttt)
REVERT: D 1040 MET cc_start: 0.2445 (tpt) cc_final: 0.1975 (tpt)
REVERT: D 1151 LYS cc_start: 0.7827 (mppt) cc_final: 0.7535 (mmtm)
REVERT: M  270 GLU cc_start: 0.6757 (tp30) cc_final: 0.6352 (tp30)
REVERT: M  455 ARG cc_start: 0.5149 (tpt90) cc_final: 0.3032 (tmm160)
  outliers start: 66
  outliers final: 43
  residues processed: 375
  average time/residue: 0.3878
  time to fit residues: 235.0795
Evaluate side-chains
  342 residues out of total 3113 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 296
  time to evaluate  : 3.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain B residue   26 VAL
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain C residue   47 TYR
Chi-restraints excluded: chain C residue   80 PHE
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  177 ILE
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain C residue  539 THR
Chi-restraints excluded: chain C residue  680 LEU
Chi-restraints excluded: chain C residue  704 MET
Chi-restraints excluded: chain C residue  900 LYS
Chi-restraints excluded: chain C residue  953 LEU
Chi-restraints excluded: chain C residue  967 LEU
Chi-restraints excluded: chain C residue 1049 ILE
Chi-restraints excluded: chain C residue 1052 VAL
Chi-restraints excluded: chain C residue 1115 THR
Chi-restraints excluded: chain C residue 1163 THR
Chi-restraints excluded: chain C residue 1241 ASP
Chi-restraints excluded: chain C residue 1293 VAL
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue   61 ILE
Chi-restraints excluded: chain D residue   70 CYS
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  114 ILE
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  177 ASP
Chi-restraints excluded: chain D residue  239 LEU
Chi-restraints excluded: chain D residue  350 SER
Chi-restraints excluded: chain D residue  408 VAL
Chi-restraints excluded: chain D residue  412 LEU
Chi-restraints excluded: chain D residue  415 VAL
Chi-restraints excluded: chain D residue  434 ILE
Chi-restraints excluded: chain D residue  506 VAL
Chi-restraints excluded: chain D residue  772 TYR
Chi-restraints excluded: chain D residue  858 VAL
Chi-restraints excluded: chain D residue  915 ILE
Chi-restraints excluded: chain D residue  921 GLN
Chi-restraints excluded: chain D residue 1292 LEU
Chi-restraints excluded: chain D residue 1320 ILE
Chi-restraints excluded: chain E residue   47 THR
Chi-restraints excluded: chain M residue  210 THR
Chi-restraints excluded: chain M residue  355 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 371
   random chunks:
   chunk 325 optimal weight:    0.9980
   chunk 342 optimal weight:    0.2980
   chunk 312 optimal weight:    5.9990
   chunk 333 optimal weight:    0.0570
   chunk 200 optimal weight:    7.9990
   chunk 145 optimal weight:    6.9990
   chunk 261 optimal weight:    7.9990
   chunk 102 optimal weight:    8.9990
   chunk 301 optimal weight:    0.0070
   chunk 315 optimal weight:    8.9990
   chunk 332 optimal weight:    0.9990
   overall best weight:    0.4718

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

Flipped N/Q/H residues before XYZ refinement:
** A  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 186 GLN
** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1244 GLN
** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 387 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7051
moved from start:          1.3191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  29301  Z= 0.183
  Angle     :  0.690  13.833  40250  Z= 0.339
  Chirality :  0.043   0.207   4788
  Planarity :  0.005   0.078   4929
  Dihedral  : 16.213 173.325   5044
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 16.30
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  5.56 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 34.70 %
    Favored  : 63.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.67 %
    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: -0.41 (0.14), residues: 3612
  helix:  1.00 (0.14), residues: 1317
  sheet:  0.42 (0.29), residues: 346
  loop : -1.34 (0.14), residues: 1949

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP D 236 
 HIS   0.009   0.001   HIS D  80 
 PHE   0.023   0.001   PHE D   7 
 TYR   0.023   0.001   TYR A 152 
 ARG   0.008   0.000   ARG D1222 

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

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

  7224 Ramachandran restraints generated.
    3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7224 Ramachandran restraints generated.
    3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  367 residues out of total 3113 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 50
    poor density    : 317
  time to evaluate  : 3.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 MET cc_start: 0.7726 (mmm) cc_final: 0.7410 (mmt)
REVERT: B   51 MET cc_start: 0.7238 (tpp) cc_final: 0.6886 (tpp)
REVERT: C   47 TYR cc_start: 0.6519 (OUTLIER) cc_final: 0.6222 (p90)
REVERT: C   80 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.6974 (m-80)
REVERT: C  523 GLU cc_start: 0.5616 (mt-10) cc_final: 0.5317 (mt-10)
REVERT: C  900 LYS cc_start: 0.6447 (OUTLIER) cc_final: 0.5685 (mttt)
REVERT: C 1023 HIS cc_start: 0.8212 (m90) cc_final: 0.7947 (m90)
REVERT: D  400 MET cc_start: 0.6894 (tmm) cc_final: 0.6638 (ttt)
REVERT: D  500 ILE cc_start: 0.8265 (mp) cc_final: 0.8047 (mt)
REVERT: D 1040 MET cc_start: 0.2400 (tpt) cc_final: 0.1976 (tpt)
REVERT: M  154 LEU cc_start: 0.4798 (mt) cc_final: 0.4575 (tp)
REVERT: M  270 GLU cc_start: 0.6624 (tp30) cc_final: 0.6230 (tp30)
  outliers start: 50
  outliers final: 36
  residues processed: 353
  average time/residue: 0.3718
  time to fit residues: 217.4283
Evaluate side-chains
  332 residues out of total 3113 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 293
  time to evaluate  : 3.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain B residue   26 VAL
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain C residue   47 TYR
Chi-restraints excluded: chain C residue   80 PHE
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  539 THR
Chi-restraints excluded: chain C residue  680 LEU
Chi-restraints excluded: chain C residue  704 MET
Chi-restraints excluded: chain C residue  900 LYS
Chi-restraints excluded: chain C residue  967 LEU
Chi-restraints excluded: chain C residue 1049 ILE
Chi-restraints excluded: chain C residue 1052 VAL
Chi-restraints excluded: chain C residue 1115 THR
Chi-restraints excluded: chain C residue 1241 ASP
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue   61 ILE
Chi-restraints excluded: chain D residue   70 CYS
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  114 ILE
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  177 ASP
Chi-restraints excluded: chain D residue  338 PHE
Chi-restraints excluded: chain D residue  408 VAL
Chi-restraints excluded: chain D residue  412 LEU
Chi-restraints excluded: chain D residue  415 VAL
Chi-restraints excluded: chain D residue  434 ILE
Chi-restraints excluded: chain D residue  474 LEU
Chi-restraints excluded: chain D residue  506 VAL
Chi-restraints excluded: chain D residue  674 THR
Chi-restraints excluded: chain D residue  772 TYR
Chi-restraints excluded: chain D residue  858 VAL
Chi-restraints excluded: chain D residue  915 ILE
Chi-restraints excluded: chain D residue  921 GLN
Chi-restraints excluded: chain D residue 1292 LEU
Chi-restraints excluded: chain D residue 1320 ILE
Chi-restraints excluded: chain M residue  210 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 371
   random chunks:
   chunk 218 optimal weight:    9.9990
   chunk 352 optimal weight:    4.9990
   chunk 215 optimal weight:    5.9990
   chunk 167 optimal weight:    5.9990
   chunk 244 optimal weight:    5.9990
   chunk 369 optimal weight:    8.9990
   chunk 340 optimal weight:    5.9990
   chunk 294 optimal weight:   30.0000
   chunk 30 optimal weight:   10.0000
   chunk 227 optimal weight:    3.9990
   chunk 180 optimal weight:    0.7980
   overall best weight:    4.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 314 ASN
** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 760 ASN
C1116 HIS
C1175 ASN
** C1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1313 HIS
** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 504 GLN
** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1249 ASN
E  15 ASN
M 202 GLN
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 290 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          1.4852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.128  29301  Z= 0.356
  Angle     :  0.813  29.572  40250  Z= 0.407
  Chirality :  0.047   0.262   4788
  Planarity :  0.006   0.124   4929
  Dihedral  : 16.386 170.931   5044
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 21.11
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  7.28 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 34.43 %
    Favored  : 63.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.67 %
    Twisted General : 0.03 %

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: -0.69 (0.14), residues: 3612
  helix:  0.74 (0.14), residues: 1307
  sheet:  0.13 (0.28), residues: 357
  loop : -1.47 (0.14), residues: 1948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP C 807 
 HIS   0.011   0.002   HIS D1366 
 PHE   0.070   0.003   PHE M 354 
 TYR   0.031   0.002   TYR C  26 
 ARG   0.015   0.001   ARG A 150 

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

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

  7224 Ramachandran restraints generated.
    3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7224 Ramachandran restraints generated.
    3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  347 residues out of total 3113 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 64
    poor density    : 283
  time to evaluate  : 3.080 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 HIS cc_start: 0.8225 (OUTLIER) cc_final: 0.7348 (t-90)
REVERT: B   51 MET cc_start: 0.7652 (tpp) cc_final: 0.6904 (tpp)
REVERT: C   80 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7341 (m-80)
REVERT: C  430 LYS cc_start: 0.6938 (tptt) cc_final: 0.6683 (mptt)
REVERT: D  500 ILE cc_start: 0.8336 (mp) cc_final: 0.8078 (mt)
REVERT: D 1040 MET cc_start: 0.3054 (tpt) cc_final: 0.2210 (tpt)
  outliers start: 64
  outliers final: 41
  residues processed: 333
  average time/residue: 0.3774
  time to fit residues: 203.7396
Evaluate side-chains
  291 residues out of total 3113 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 248
  time to evaluate  : 3.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain B residue   26 VAL
Chi-restraints excluded: chain B residue   37 HIS
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain C residue   80 PHE
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  177 ILE
Chi-restraints excluded: chain C residue  680 LEU
Chi-restraints excluded: chain C residue  900 LYS
Chi-restraints excluded: chain C residue  967 LEU
Chi-restraints excluded: chain C residue 1049 ILE
Chi-restraints excluded: chain C residue 1115 THR
Chi-restraints excluded: chain C residue 1154 ASP
Chi-restraints excluded: chain C residue 1241 ASP
Chi-restraints excluded: chain C residue 1293 VAL
Chi-restraints excluded: chain D residue   61 ILE
Chi-restraints excluded: chain D residue   70 CYS
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  114 ILE
Chi-restraints excluded: chain D residue  177 ASP
Chi-restraints excluded: chain D residue  239 LEU
Chi-restraints excluded: chain D residue  338 PHE
Chi-restraints excluded: chain D residue  408 VAL
Chi-restraints excluded: chain D residue  415 VAL
Chi-restraints excluded: chain D residue  422 LEU
Chi-restraints excluded: chain D residue  506 VAL
Chi-restraints excluded: chain D residue  674 THR
Chi-restraints excluded: chain D residue  772 TYR
Chi-restraints excluded: chain D residue  858 VAL
Chi-restraints excluded: chain D residue  910 ASN
Chi-restraints excluded: chain D residue  915 ILE
Chi-restraints excluded: chain D residue  918 ILE
Chi-restraints excluded: chain D residue  921 GLN
Chi-restraints excluded: chain D residue 1292 LEU
Chi-restraints excluded: chain D residue 1320 ILE
Chi-restraints excluded: chain E residue   11 GLU
Chi-restraints excluded: chain E residue   44 ASP
Chi-restraints excluded: chain M residue  199 LEU
Chi-restraints excluded: chain M residue  210 THR
Chi-restraints excluded: chain M residue  363 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 371
   random chunks:
   chunk 233 optimal weight:    0.7980
   chunk 313 optimal weight:    0.9990
   chunk 90 optimal weight:    6.9990
   chunk 271 optimal weight:    0.7980
   chunk 43 optimal weight:    5.9990
   chunk 81 optimal weight:    8.9990
   chunk 294 optimal weight:   30.0000
   chunk 123 optimal weight:    5.9990
   chunk 302 optimal weight:    5.9990
   chunk 37 optimal weight:   10.0000
   chunk 54 optimal weight:    3.9990
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 314 ASN
** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 504 GLN
** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 202 GLN
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.086508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.062160 restraints weight = 114029.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 4.26
r_work: 0.3056 rms_B_bonded: 4.74 restraints_weight: 0.5000
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3061
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3061
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          1.5215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  29301  Z= 0.239
  Angle     :  0.738  12.982  40250  Z= 0.366
  Chirality :  0.045   0.270   4788
  Planarity :  0.005   0.080   4929
  Dihedral  : 16.319 171.985   5044
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 18.07
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  6.20 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 35.93 %
    Favored  : 62.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.67 %
    Twisted General : 0.03 %

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: -0.55 (0.14), residues: 3612
  helix:  0.90 (0.14), residues: 1314
  sheet:  0.12 (0.28), residues: 357
  loop : -1.40 (0.14), residues: 1941

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP D 236 
 HIS   0.008   0.001   HIS D  80 
 PHE   0.034   0.002   PHE C 390 
 TYR   0.028   0.002   TYR A 152 
 ARG   0.017   0.001   ARG C 454 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7081.14 seconds
wall clock time: 127 minutes 18.81 seconds (7638.81 seconds total)