Starting phenix.real_space_refine
on Fri Aug  9 09:11:17 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu8_29455/08_2024/8fu8_29455_neut.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu8_29455/08_2024/8fu8_29455.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.08
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu8_29455/08_2024/8fu8_29455.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu8_29455/08_2024/8fu8_29455.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu8_29455/08_2024/8fu8_29455_neut.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu8_29455/08_2024/8fu8_29455_neut.cif"
  }
  resolution = 3.08
  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: 4
    Type Number    sf(0)   Gaussians
     S     109      5.16       5
     C   16192      2.51       5
     N    4177      2.21       5
     O    4991      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR   28": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   86": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   92": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU   96": "OE1" <-> "OE2"
    Residue "A PHE  135": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  159": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  177": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  185": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  191": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  249": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  297": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  313": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  322": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  349": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  358": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  361": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  380": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  405": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  433": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  437": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  448": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  449": "OE1" <-> "OE2"
    Residue "A TYR  492": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  499": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  527": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  549": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  562": "OD1" <-> "OD2"
    Residue "A PHE  576": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  620": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  644": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  679": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  743": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  766": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  773": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  781": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  786": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  839": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  857": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  872": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  888": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  901": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  954": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR 1031": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR 1051": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1059": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1073": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1079": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1087": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   28": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   38": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   65": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   79": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   86": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   92": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  133": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  135": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  151": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  185": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  191": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  211": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  229": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  239": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  249": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  313": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  322": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  326": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  335": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  349": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  358": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  361": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  364": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  376": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  380": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  435": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  448": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  470": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  576": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  620": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  644": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  679": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  743": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  766": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  773": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  781": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  786": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  807": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  857": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  872": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  901": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  954": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR 1031": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR 1051": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE 1059": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE 1073": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE 1079": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR   28": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR   37": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   65": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   92": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  133": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  136": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  151": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  159": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  177": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  185": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  191": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  229": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  249": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  250": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  297": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  313": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  322": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  349": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  358": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  361": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  376": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  433": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  435": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  440": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  448": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  470": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  473": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  481": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  492": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  499": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  527": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  549": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  644": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  679": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  743": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  766": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  773": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  781": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  786": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  857": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  872": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  888": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  901": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  954": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR 1031": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR 1051": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE 1059": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE 1079": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE 1087": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.09s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib"
  Total number of atoms: 25469
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 8183
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1046, 8183
          Classifications: {'peptide': 1046}
          Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 989}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 8360
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1069, 8360
          Classifications: {'peptide': 1069}
          Link IDs: {'PTRANS': 55, 'TRANS': 1013}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 8211
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1050, 8211
          Classifications: {'peptide': 1050}
          Link IDs: {'PTRANS': 53, 'TRANS': 996}
          Chain breaks: 5
    Chain: "A"
      Number of atoms: 253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 253
          Unusual residues: {'NAG': 17}
          Classifications: {'undetermined': 17}
          Link IDs: {None: 16}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 224
          Unusual residues: {'NAG': 15}
          Classifications: {'undetermined': 15}
          Link IDs: {None: 14}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 238
          Unusual residues: {'NAG': 16}
          Classifications: {'undetermined': 16}
          Link IDs: {None: 15}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 15.94, per 1000 atoms: 0.63
  Number of scatterers: 25469
  At special positions: 0
  Unit cell: (137.313, 155.621, 163.111, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S     109     16.00
     O    4991      8.00
     N    4177      7.00
     C   16192      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
  Links applied
    NAG-ASN
      " NAG A1206 " - " ASN A 225 "
      " NAG A1215 " - " ASN A1082 "
      " NAG B1210 " - " ASN B  61 "
      " NAG C1204 " - " ASN C 225 "
      " NAG C1212 " - " ASN C 315 "
  Time building additional restraints: 11.15
  Conformation dependent library (CDL) restraints added in 5.1 seconds
  

  6274 Ramachandran restraints generated.
    3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5920

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 42 sheets defined
      23.8% alpha, 27.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 3.68
  Creating SS restraints...
    Processing helix  chain 'A' and resid 278 through 288
    Processing helix  chain 'A' and resid 322 through 327
    Processing helix  chain 'A' and resid 333 through 337
      removed outlier: 3.529A  pdb=" N   TRP A 337 " --> pdb=" O   VAL A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 370 through 373
    Processing helix  chain 'A' and resid 390 through 395
    Processing helix  chain 'A' and resid 400 through 406
    Processing helix  chain 'A' and resid 607 through 612
    Processing helix  chain 'A' and resid 721 through 728
    Processing helix  chain 'A' and resid 730 through 738
    Processing helix  chain 'A' and resid 739 through 741
      No H-bonds generated for 'chain 'A' and resid 739 through 741'
    Processing helix  chain 'A' and resid 742 through 767
      removed outlier: 3.532A  pdb=" N   ASP A 759 " --> pdb=" O   ALA A 755 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 800 through 810
    Processing helix  chain 'A' and resid 850 through 869
    Processing helix  chain 'A' and resid 870 through 874
    Processing helix  chain 'A' and resid 881 through 892
    Processing helix  chain 'A' and resid 896 through 902
      removed outlier: 4.132A  pdb=" N   LEU A 900 " --> pdb=" O   THR A 896 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 903 through 925
    Processing helix  chain 'A' and resid 929 through 949
      removed outlier: 3.946A  pdb=" N   VAL A 935 " --> pdb=" O   LYS A 931 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 950 through 952
      No H-bonds generated for 'chain 'A' and resid 950 through 952'
    Processing helix  chain 'A' and resid 960 through 966
    Processing helix  chain 'A' and resid 969 through 1017
      removed outlier: 4.295A  pdb=" N   VAL A 975 " --> pdb=" O   PRO A 971 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1125 through 1130
    Processing helix  chain 'B' and resid 277 through 287
      removed outlier: 4.051A  pdb=" N   SER B 281 " --> pdb=" O   LEU B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 327
    Processing helix  chain 'B' and resid 333 through 337
      removed outlier: 3.931A  pdb=" N   TRP B 337 " --> pdb=" O   VAL B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 349 through 354
    Processing helix  chain 'B' and resid 367 through 372
      removed outlier: 4.292A  pdb=" N   ASN B 372 " --> pdb=" O   PRO B 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 585 through 589
    Processing helix  chain 'B' and resid 603 through 608
    Processing helix  chain 'B' and resid 609 through 613
    Processing helix  chain 'B' and resid 614 through 619
      removed outlier: 3.655A  pdb=" N   VAL B 619 " --> pdb=" O   PRO B 615 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 721 through 727
    Processing helix  chain 'B' and resid 730 through 737
    Processing helix  chain 'B' and resid 738 through 741
    Processing helix  chain 'B' and resid 742 through 767
      removed outlier: 3.751A  pdb=" N   ASP B 759 " --> pdb=" O   ALA B 755 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 800 through 810
    Processing helix  chain 'B' and resid 850 through 869
    Processing helix  chain 'B' and resid 870 through 874
    Processing helix  chain 'B' and resid 881 through 891
    Processing helix  chain 'B' and resid 896 through 902
      removed outlier: 4.185A  pdb=" N   LEU B 900 " --> pdb=" O   THR B 896 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 903 through 923
      removed outlier: 3.802A  pdb=" N   ILE B 918 " --> pdb=" O   ALA B 914 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   GLN B 919 " --> pdb=" O   ILE B 915 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ASP B 920 " --> pdb=" O   GLY B 916 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 929 through 949
      removed outlier: 3.894A  pdb=" N   VAL B 935 " --> pdb=" O   LYS B 931 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 950 through 952
      No H-bonds generated for 'chain 'B' and resid 950 through 952'
    Processing helix  chain 'B' and resid 961 through 966
    Processing helix  chain 'B' and resid 969 through 1017
      removed outlier: 3.897A  pdb=" N   VAL B 975 " --> pdb=" O   PRO B 971 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1125 through 1130
      removed outlier: 3.670A  pdb=" N   LEU B1129 " --> pdb=" O   LEU B1125 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 278 through 288
    Processing helix  chain 'C' and resid 348 through 354
      removed outlier: 4.097A  pdb=" N   LEU C 352 " --> pdb=" O   ASP C 348 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 370 through 373
    Processing helix  chain 'C' and resid 721 through 727
    Processing helix  chain 'C' and resid 730 through 738
      removed outlier: 4.227A  pdb=" N   LEU C 736 " --> pdb=" O   GLU C 732 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU C 738 " --> pdb=" O   SER C 734 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 739 through 741
      No H-bonds generated for 'chain 'C' and resid 739 through 741'
    Processing helix  chain 'C' and resid 742 through 767
      removed outlier: 3.809A  pdb=" N   ASP C 759 " --> pdb=" O   ALA C 755 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 800 through 810
    Processing helix  chain 'C' and resid 850 through 868
    Processing helix  chain 'C' and resid 870 through 874
    Processing helix  chain 'C' and resid 881 through 892
    Processing helix  chain 'C' and resid 896 through 902
      removed outlier: 4.277A  pdb=" N   LEU C 900 " --> pdb=" O   THR C 896 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 903 through 923
    Processing helix  chain 'C' and resid 925 through 928
    Processing helix  chain 'C' and resid 929 through 949
      removed outlier: 3.949A  pdb=" N   VAL C 935 " --> pdb=" O   LYS C 931 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 950 through 952
      No H-bonds generated for 'chain 'C' and resid 950 through 952'
    Processing helix  chain 'C' and resid 960 through 968
    Processing helix  chain 'C' and resid 970 through 1017
      removed outlier: 3.876A  pdb=" N   VAL C 975 " --> pdb=" O   PRO C 971 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1125 through 1130
    Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30
      removed outlier: 7.883A  pdb=" N   ASN A  61 " --> pdb=" O   TYR A 253 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   TYR A 253 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   SER A 196 " --> pdb=" O   PRO A 216 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   VAL A  36 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43
    Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55
      removed outlier: 3.757A  pdb=" N   ASP A 271 " --> pdb=" O   LYS A 262 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85
    Processing sheet with id=AA5, first strand: chain 'A' and resid 295 through 300
      removed outlier: 6.951A  pdb=" N   VAL A 579 " --> pdb=" O   THR A 299 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 312
      removed outlier: 4.782A  pdb=" N   GLU A 308 " --> pdb=" O   CYS A 522 " (cutoff:3.500A)
      removed outlier: 5.758A  pdb=" N   ASP A 558 " --> pdb=" O   ILE A 571 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   PHE A 549 " --> pdb=" O   PHE B  43 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 338 through 342
      removed outlier: 3.642A  pdb=" N   VAL A 379 " --> pdb=" O   ILE A 342 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   CYS A 345 " --> pdb=" O   CYS A 509 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 338 through 342
      removed outlier: 3.642A  pdb=" N   VAL A 379 " --> pdb=" O   ILE A 342 " (cutoff:3.500A)
      removed outlier: 5.065A  pdb=" N   ASN A 378 " --> pdb=" O   GLU A 500 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   GLU A 500 " --> pdb=" O   ASN A 378 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 436 through 437
      removed outlier: 4.589A  pdb=" N   LEU A 436 " --> pdb=" O   LEU A 476 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 638 through 639
      removed outlier: 6.587A  pdb=" N   ILE A 654 " --> pdb=" O   ILE A 650 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 685 through 688
      removed outlier: 6.571A  pdb=" N   ALA A 685 " --> pdb=" O   ILE B 772 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   LYS B 774 " --> pdb=" O   ALA A 685 " (cutoff:3.500A)
      removed outlier: 7.281A  pdb=" N   ASN A 687 " --> pdb=" O   LYS B 774 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'A' and resid 695 through 698
      removed outlier: 3.740A  pdb=" N   ALA A1062 " --> pdb=" O   PHE A1079 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   PHE A1079 " --> pdb=" O   ALA A1062 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 712
      removed outlier: 5.866A  pdb=" N   TYR A1051 " --> pdb=" O   HIS A1032 " (cutoff:3.500A)
      removed outlier: 5.721A  pdb=" N   HIS A1032 " --> pdb=" O   TYR A1051 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 720
      removed outlier: 4.164A  pdb=" N   LYS A 717 " --> pdb=" O   LEU A 845 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 771 through 774
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1104 through 1109
      removed outlier: 4.904A  pdb=" N   ALA A1071 " --> pdb=" O   SER A1107 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 29 through 31
      removed outlier: 7.874A  pdb=" N   ASN B  61 " --> pdb=" O   TYR B 253 " (cutoff:3.500A)
      removed outlier: 5.888A  pdb=" N   TYR B 253 " --> pdb=" O   ASN B  61 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   SER B 196 " --> pdb=" O   PRO B 216 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55
      removed outlier: 7.515A  pdb=" N   THR B 258 " --> pdb=" O   ASP B 274 " (cutoff:3.500A)
      removed outlier: 5.180A  pdb=" N   ASP B 274 " --> pdb=" O   THR B 258 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   LEU B 260 " --> pdb=" O   ALA B 272 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   ALA B 272 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   LYS B 262 " --> pdb=" O   THR B 270 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85
      removed outlier: 3.509A  pdb=" N   PHE B 159 " --> pdb=" O   VAL B 130 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 295 through 303
      removed outlier: 5.379A  pdb=" N   ILE B 296 " --> pdb=" O   THR B 583 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   THR B 583 " --> pdb=" O   ILE B 296 " (cutoff:3.500A)
      removed outlier: 5.691A  pdb=" N   GLN B 298 " --> pdb=" O   VAL B 581 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   VAL B 581 " --> pdb=" O   GLN B 298 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   SER B 300 " --> pdb=" O   VAL B 579 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   GLY B 578 " --> pdb=" O   GLN B 597 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 309 through 312
      removed outlier: 5.227A  pdb=" N   ASP B 558 " --> pdb=" O   ILE B 571 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   ALA B 559 " --> pdb=" O   GLY B 550 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   PHE B 549 " --> pdb=" O   PHE C  43 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 338 through 342
      removed outlier: 6.586A  pdb=" N   CYS B 345 " --> pdb=" O   CYS B 509 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 338 through 342
      removed outlier: 5.432A  pdb=" N   ASN B 378 " --> pdb=" O   GLU B 500 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   GLU B 500 " --> pdb=" O   ASN B 378 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'B' and resid 638 through 639
      removed outlier: 6.604A  pdb=" N   ILE B 654 " --> pdb=" O   ILE B 650 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'B' and resid 686 through 688
    Processing sheet with id=AC8, first strand: chain 'B' and resid 695 through 712
      removed outlier: 6.560A  pdb=" N   SER B 695 " --> pdb=" O   THR B1060 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   THR B1060 " --> pdb=" O   SER B 695 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   ALA B 697 " --> pdb=" O   ASN B1058 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   ASN B1058 " --> pdb=" O   ALA B 697 " (cutoff:3.500A)
      removed outlier: 6.049A  pdb=" N   GLU B1056 " --> pdb=" O   PRO B 699 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   TYR B1051 " --> pdb=" O   HIS B1032 " (cutoff:3.500A)
      removed outlier: 5.694A  pdb=" N   HIS B1032 " --> pdb=" O   TYR B1051 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 695 through 712
      removed outlier: 6.560A  pdb=" N   SER B 695 " --> pdb=" O   THR B1060 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   THR B1060 " --> pdb=" O   SER B 695 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   ALA B 697 " --> pdb=" O   ASN B1058 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   ASN B1058 " --> pdb=" O   ALA B 697 " (cutoff:3.500A)
      removed outlier: 6.049A  pdb=" N   GLU B1056 " --> pdb=" O   PRO B 699 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ALA B1062 " --> pdb=" O   PHE B1079 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   PHE B1079 " --> pdb=" O   ALA B1062 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   GLN B1090 " --> pdb=" O   GLU B1095 " (cutoff:3.500A)
      removed outlier: 6.013A  pdb=" N   GLU B1095 " --> pdb=" O   GLN B1090 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'B' and resid 717 through 720
      removed outlier: 4.269A  pdb=" N   LYS B 717 " --> pdb=" O   LEU B 845 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'B' and resid 1104 through 1109
      removed outlier: 4.785A  pdb=" N   ALA B1071 " --> pdb=" O   SER B1107 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'C' and resid 29 through 32
      removed outlier: 3.546A  pdb=" N   SER C  60 " --> pdb=" O   SER C  31 " (cutoff:3.500A)
      removed outlier: 8.484A  pdb=" N   ASN C  61 " --> pdb=" O   TYR C 253 " (cutoff:3.500A)
      removed outlier: 6.052A  pdb=" N   TYR C 253 " --> pdb=" O   ASN C  61 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   PHE C 192 " --> pdb=" O   ASP C 219 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   ASP C 219 " --> pdb=" O   PHE C 192 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   ILE C 194 " --> pdb=" O   LEU C 217 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55
      removed outlier: 7.367A  pdb=" N   THR C 258 " --> pdb=" O   ASP C 274 " (cutoff:3.500A)
      removed outlier: 5.109A  pdb=" N   ASP C 274 " --> pdb=" O   THR C 258 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   LEU C 260 " --> pdb=" O   ALA C 272 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   ALA C 272 " --> pdb=" O   LEU C 260 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   LYS C 262 " --> pdb=" O   THR C 270 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'C' and resid 159 through 163
      removed outlier: 3.890A  pdb=" N   GLY C 103 " --> pdb=" O   LEU C 232 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'C' and resid 178 through 180
    Processing sheet with id=AD7, first strand: chain 'C' and resid 295 through 303
      removed outlier: 5.209A  pdb=" N   ILE C 296 " --> pdb=" O   THR C 583 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   THR C 583 " --> pdb=" O   ILE C 296 " (cutoff:3.500A)
      removed outlier: 5.661A  pdb=" N   GLN C 298 " --> pdb=" O   VAL C 581 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   VAL C 581 " --> pdb=" O   GLN C 298 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   GLY C 578 " --> pdb=" O   GLN C 597 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'C' and resid 308 through 312
      removed outlier: 3.961A  pdb=" N   GLU C 308 " --> pdb=" O   CYS C 522 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'C' and resid 338 through 342
      removed outlier: 3.901A  pdb=" N   VAL C 379 " --> pdb=" O   ILE C 342 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   CYS C 345 " --> pdb=" O   CYS C 509 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'C' and resid 338 through 342
      removed outlier: 3.901A  pdb=" N   VAL C 379 " --> pdb=" O   ILE C 342 " (cutoff:3.500A)
      removed outlier: 5.102A  pdb=" N   ASN C 378 " --> pdb=" O   GLU C 500 " (cutoff:3.500A)
      removed outlier: 4.744A  pdb=" N   GLU C 500 " --> pdb=" O   ASN C 378 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   TYR C 492 " --> pdb=" O   ILE C 386 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'C' and resid 638 through 639
      removed outlier: 6.576A  pdb=" N   ILE C 654 " --> pdb=" O   ILE C 650 " (cutoff:3.500A)
    Processing sheet with id=AE3, first strand: chain 'C' and resid 695 through 712
      removed outlier: 7.045A  pdb=" N   GLN C1055 " --> pdb=" O   THR C 700 " (cutoff:3.500A)
      removed outlier: 5.860A  pdb=" N   PHE C 702 " --> pdb=" O   PRO C1053 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   ILE C 704 " --> pdb=" O   TYR C1051 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   TYR C1051 " --> pdb=" O   ILE C 704 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   VAL C 706 " --> pdb=" O   VAL C1049 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   VAL C1049 " --> pdb=" O   VAL C 706 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   THR C 708 " --> pdb=" O   LEU C1047 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   LEU C1047 " --> pdb=" O   THR C 708 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   ILE C 710 " --> pdb=" O   VAL C1045 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   VAL C1045 " --> pdb=" O   ILE C 710 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   GLY C1043 " --> pdb=" O   PRO C 712 " (cutoff:3.500A)
      removed outlier: 5.991A  pdb=" N   TYR C1051 " --> pdb=" O   HIS C1032 " (cutoff:3.500A)
      removed outlier: 5.657A  pdb=" N   HIS C1032 " --> pdb=" O   TYR C1051 " (cutoff:3.500A)
    Processing sheet with id=AE4, first strand: chain 'C' and resid 695 through 712
      removed outlier: 7.045A  pdb=" N   GLN C1055 " --> pdb=" O   THR C 700 " (cutoff:3.500A)
      removed outlier: 5.860A  pdb=" N   PHE C 702 " --> pdb=" O   PRO C1053 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   ILE C 704 " --> pdb=" O   TYR C1051 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   TYR C1051 " --> pdb=" O   ILE C 704 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   VAL C 706 " --> pdb=" O   VAL C1049 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   VAL C1049 " --> pdb=" O   VAL C 706 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   THR C 708 " --> pdb=" O   LEU C1047 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   LEU C1047 " --> pdb=" O   THR C 708 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   ILE C 710 " --> pdb=" O   VAL C1045 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   VAL C1045 " --> pdb=" O   ILE C 710 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   GLY C1043 " --> pdb=" O   PRO C 712 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ALA C1062 " --> pdb=" O   PHE C1079 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   PHE C1079 " --> pdb=" O   ALA C1062 " (cutoff:3.500A)
    Processing sheet with id=AE5, first strand: chain 'C' and resid 717 through 720
      removed outlier: 4.381A  pdb=" N   LYS C 717 " --> pdb=" O   LEU C 845 " (cutoff:3.500A)
    Processing sheet with id=AE6, first strand: chain 'C' and resid 1104 through 1109
      removed outlier: 6.100A  pdb=" N   ALA C1071 " --> pdb=" O   SER C1107 " (cutoff:3.500A)

    1030 hydrogen bonds defined for protein.
    2787 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 12.54

  Time building geometry restraints manager: 12.12 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 4972
        1.32 -     1.45: 6444
        1.45 -     1.57: 14481
        1.57 -     1.69: 17
        1.69 -     1.82: 139
  Bond restraints: 26053
  Sorted by residual:
  bond pdb=" C1  NAG B1203 "
       pdb=" O1  NAG B1203 "
    ideal  model  delta    sigma   weight residual
    1.376  1.483 -0.107 2.00e-02 2.50e+03 2.84e+01
  bond pdb=" C1  NAG B1204 "
       pdb=" O1  NAG B1204 "
    ideal  model  delta    sigma   weight residual
    1.376  1.482 -0.106 2.00e-02 2.50e+03 2.79e+01
  bond pdb=" C1  NAG C1215 "
       pdb=" O1  NAG C1215 "
    ideal  model  delta    sigma   weight residual
    1.376  1.481 -0.105 2.00e-02 2.50e+03 2.78e+01
  bond pdb=" C1  NAG A1211 "
       pdb=" O1  NAG A1211 "
    ideal  model  delta    sigma   weight residual
    1.376  1.481 -0.105 2.00e-02 2.50e+03 2.77e+01
  bond pdb=" C1  NAG C1213 "
       pdb=" O1  NAG C1213 "
    ideal  model  delta    sigma   weight residual
    1.376  1.481 -0.105 2.00e-02 2.50e+03 2.75e+01
  ... (remaining 26048 not shown)

  Histogram of bond angle deviations from ideal:
       99.83 -   106.68: 775
      106.68 -   113.53: 14246
      113.53 -   120.38: 9909
      120.38 -   127.24: 10440
      127.24 -   134.09: 114
  Bond angle restraints: 35484
  Sorted by residual:
  angle pdb=" C   LEU C 207 "
        pdb=" N   PRO C 208 "
        pdb=" CA  PRO C 208 "
      ideal   model   delta    sigma   weight residual
     119.56  128.29   -8.73 1.02e+00 9.61e-01 7.33e+01
  angle pdb=" C   LEU C 845 "
        pdb=" N   PRO C 846 "
        pdb=" CA  PRO C 846 "
      ideal   model   delta    sigma   weight residual
     119.66  125.70   -6.04 7.20e-01 1.93e+00 7.04e+01
  angle pdb=" C   PRO A  25 "
        pdb=" N   PRO A  26 "
        pdb=" CA  PRO A  26 "
      ideal   model   delta    sigma   weight residual
     120.31  128.42   -8.11 9.80e-01 1.04e+00 6.84e+01
  angle pdb=" C   LEU A 207 "
        pdb=" N   PRO A 208 "
        pdb=" CA  PRO A 208 "
      ideal   model   delta    sigma   weight residual
     120.21  128.06   -7.85 9.60e-01 1.09e+00 6.69e+01
  angle pdb=" C   THR A 775 "
        pdb=" N   PRO A 776 "
        pdb=" CA  PRO A 776 "
      ideal   model   delta    sigma   weight residual
     119.66  125.45   -5.79 7.20e-01 1.93e+00 6.46e+01
  ... (remaining 35479 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 15529
       17.96 -    35.92: 457
       35.92 -    53.88: 100
       53.88 -    71.84: 42
       71.84 -    89.80: 17
  Dihedral angle restraints: 16145
    sinusoidal: 6935
      harmonic: 9210
  Sorted by residual:
  dihedral pdb=" CA  THR B 583 "
           pdb=" C   THR B 583 "
           pdb=" N   PRO B 584 "
           pdb=" CA  PRO B 584 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.27   19.73     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  THR C 583 "
           pdb=" C   THR C 583 "
           pdb=" N   PRO C 584 "
           pdb=" CA  PRO C 584 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.96   17.04     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CA  SER C 367 "
           pdb=" C   SER C 367 "
           pdb=" N   PRO C 368 "
           pdb=" CA  PRO C 368 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.45   16.55     0      5.00e+00 4.00e-02 1.10e+01
  ... (remaining 16142 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.987: 4139
       0.987 -    1.975: 0
       1.975 -    2.962: 0
       2.962 -    3.949: 0
       3.949 -    4.937: 1
  Chirality restraints: 4140
  Sorted by residual:
  chirality pdb=" C1  NAG A1206 "
            pdb=" ND2 ASN A 225 "
            pdb=" C2  NAG A1206 "
            pdb=" O5  NAG A1206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40    2.54   -4.94 2.00e-01 2.50e+01 6.09e+02
  chirality pdb=" CG  LEU C 233 "
            pdb=" CB  LEU C 233 "
            pdb=" CD1 LEU C 233 "
            pdb=" CD2 LEU C 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.97    0.38 2.00e-01 2.50e+01 3.61e+00
  chirality pdb=" C2  NAG C1204 "
            pdb=" C1  NAG C1204 "
            pdb=" C3  NAG C1204 "
            pdb=" N2  NAG C1204 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.85    0.35 2.00e-01 2.50e+01 3.13e+00
  ... (remaining 4137 not shown)

  Planarity restraints: 4530
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 437 "    0.039 2.00e-02 2.50e+03   2.11e-02 8.90e+00
        pdb=" CG  TYR A 437 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 437 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 437 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 437 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 437 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 437 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 437 "    0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 474 "    0.032 2.00e-02 2.50e+03   1.98e-02 6.86e+00
        pdb=" CG  PHE C 474 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 474 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 474 "   -0.021 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 474 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 474 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 474 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 407 "    0.032 2.00e-02 2.50e+03   1.66e-02 5.51e+00
        pdb=" CG  TYR B 407 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 407 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 407 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 407 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 407 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 407 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B 407 "    0.022 2.00e-02 2.50e+03
  ... (remaining 4527 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 8712
        2.85 -     3.36: 22932
        3.36 -     3.87: 42590
        3.87 -     4.39: 49334
        4.39 -     4.90: 82283
  Nonbonded interactions: 205851
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 541 "
            pdb=" OD2 ASP A 558 "
     model   vdw
     2.336 3.120
  nonbonded pdb=" OE2 GLU B 709 "
            pdb=" NZ  LYS B1012 "
     model   vdw
     2.340 3.120
  nonbonded pdb=" ND2 ASN B 590 "
            pdb=" OH  TYR B 658 "
     model   vdw
     2.344 3.120
  nonbonded pdb=" NZ  LYS C 428 "
            pdb=" O   PHE C 481 "
     model   vdw
     2.358 3.120
  nonbonded pdb=" NZ  LYS A 838 "
            pdb=" OD1 ASP C 558 "
     model   vdw
     2.384 3.120
  ... (remaining 205846 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 25 through 66 or resid 81 through 233 or resid 247 through \ 
 606 or resid 616 through 1130 or resid 1201 through 1203 or (resid 1204 and (na \ 
me C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name  \ 
C8 or name N2 or name O3 or name O4 or name O5 or name O6 or name O7 )) or resid \ 
 1205 through 1209 or (resid 1210 and (name C1 or name C2 or name C3 or name C4  \ 
or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or  \ 
name O5 or name O6 or name O7 )) or resid 1211 or (resid 1212 and (name C1 or na \ 
me C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name  \ 
N2 or name O3 or name O4 or name O5 or name O6 or name O7 )) or resid 1213 throu \ 
gh 1215))
  selection = (chain 'B' and (resid 25 through 66 or resid 81 through 233 or resid 247 through \ 
 606 or resid 616 through 1130 or resid 1201 through 1203 or (resid 1204 and (na \ 
me C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name  \ 
C8 or name N2 or name O3 or name O4 or name O5 or name O6 or name O7 )) or resid \ 
 1205 or (resid 1206 and (name C1 or name C2 or name C3 or name C4 or name C5 or \ 
 name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 or na \ 
me O6 or name O7 )) or resid 1207 through 1211 or (resid 1212 and (name C1 or na \ 
me C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name  \ 
N2 or name O3 or name O4 or name O5 or name O6 or name O7 )) or resid 1213 throu \ 
gh 1214 or (resid 1215 and (name C1 or name C2 or name C3 or name C4 or name C5  \ 
or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 or  \ 
name O6 or name O7 ))))
  selection = (chain 'C' and (resid 25 through 233 or resid 247 through 811 or resid 838 throu \ 
gh 1130 or resid 1201 through 1205 or (resid 1206 and (name C1 or name C2 or nam \ 
e C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O \ 
3 or name O4 or name O5 or name O6 or name O7 )) or resid 1207 through 1209 or ( \ 
resid 1210 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 o \ 
r name C7 or name C8 or name N2 or name O3 or name O4 or name O5 or name O6 or n \ 
ame O7 )) or resid 1211 through 1214 or (resid 1215 and (name C1 or name C2 or n \ 
ame C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name N2 or name \ 
 O3 or name O4 or name O5 or name O6 or name O7 ))))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             26.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.030
  Extract box with map and model:          1.250
  Check model and map are aligned:         0.210
  Set scattering table:                    0.260
  Process input model:                     75.530
  Find NCS groups from input model:        1.720
  Set up NCS constraints:                  0.110
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  108.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
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      :  0.013   0.112  26053  Z= 0.859
  Angle     :  1.290  10.018  35484  Z= 0.864
  Chirality :  0.111   4.937   4140
  Planarity :  0.005   0.033   4525
  Dihedral  : 10.271  89.798  10225
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 1.90
  Ramachandran Plot:
    Outliers :  1.05 %
    Allowed  :  5.36 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.51 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.03 %
    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: -0.39 (0.14), residues: 3137
  helix:  0.33 (0.19), residues: 658
  sheet:  0.70 (0.19), residues: 625
  loop : -0.82 (0.14), residues: 1854

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.005   TRP A  64 
 HIS   0.005   0.001   HIS A 137 
 PHE   0.032   0.003   PHE C 474 
 TYR   0.039   0.004   TYR A 437 
 ARG   0.005   0.000   ARG A 441 

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

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

  6274 Ramachandran restraints generated.
    3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6274 Ramachandran restraints generated.
    3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  507 residues out of total 2771 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 503
  time to evaluate  : 3.005 
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: A   90 VAL cc_start: 0.8635 (t) cc_final: 0.8310 (p)
REVERT: A  167 LEU cc_start: 0.7189 (mt) cc_final: 0.6859 (mm)
REVERT: A  191 TYR cc_start: 0.6777 (m-80) cc_final: 0.6454 (m-80)
REVERT: A  387 ARG cc_start: 0.6332 (ttt180) cc_final: 0.5492 (mpt180)
REVERT: A  401 LYS cc_start: 0.7271 (pttt) cc_final: 0.7071 (ptmm)
REVERT: A  435 TYR cc_start: 0.6479 (m-80) cc_final: 0.6234 (m-80)
REVERT: A  443 SER cc_start: 0.7631 (p) cc_final: 0.7323 (p)
REVERT: A  445 LEU cc_start: 0.6563 (tp) cc_final: 0.6071 (tp)
REVERT: A  641 ASN cc_start: 0.7397 (t0) cc_final: 0.7105 (t0)
REVERT: A  729 ASP cc_start: 0.7534 (p0) cc_final: 0.7138 (p0)
REVERT: A  842 LEU cc_start: 0.8296 (tp) cc_final: 0.7935 (mt)
REVERT: A 1122 TYR cc_start: 0.7719 (t80) cc_final: 0.7308 (m-10)
REVERT: B   28 TYR cc_start: 0.7287 (m-80) cc_final: 0.7075 (m-80)
REVERT: B  144 MET cc_start: 0.2138 (ttm) cc_final: 0.1574 (tpt)
REVERT: C   63 THR cc_start: 0.7975 (m) cc_final: 0.7695 (p)
REVERT: C  315 ASN cc_start: 0.5811 (OUTLIER) cc_final: 0.5464 (p0)
REVERT: C  318 ASN cc_start: 0.7191 (m-40) cc_final: 0.6940 (t0)
REVERT: C  353 TYR cc_start: 0.7035 (t80) cc_final: 0.6819 (t80)
REVERT: C  411 ASP cc_start: 0.6882 (m-30) cc_final: 0.6433 (m-30)
REVERT: C  448 PHE cc_start: 0.7845 (m-80) cc_final: 0.7615 (m-80)
REVERT: C  492 TYR cc_start: 0.6662 (m-80) cc_final: 0.5858 (m-10)
REVERT: C 1025 ASP cc_start: 0.7269 (m-30) cc_final: 0.7049 (m-30)
  outliers start: 4
  outliers final: 1
  residues processed: 507
  average time/residue: 0.4281
  time to fit residues: 330.5159
Evaluate side-chains
  245 residues out of total 2771 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 243
  time to evaluate  : 3.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  629 THR
Chi-restraints excluded: chain C residue  315 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 315
   random chunks:
   chunk 265 optimal weight:    0.9990
   chunk 238 optimal weight:    5.9990
   chunk 132 optimal weight:    9.9990
   chunk 81 optimal weight:    0.9990
   chunk 161 optimal weight:    0.6980
   chunk 127 optimal weight:    0.8980
   chunk 246 optimal weight:    0.9980
   chunk 95 optimal weight:    1.9990
   chunk 150 optimal weight:    5.9990
   chunk 183 optimal weight:    0.9990
   chunk 286 optimal weight:    8.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 137 HIS
A 139 ASN
A 198 HIS
A 209 GLN
A 354 ASN
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 424 ASN
** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 701 ASN
A1085 HIS
B  66 HIS
B 693 ASN
B1058 ASN
C 187 ASN
C 266 ASN
C 490 GLN
C1032 HIS
** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.2184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  26053  Z= 0.209
  Angle     :  0.643  13.068  35484  Z= 0.344
  Chirality :  0.049   1.064   4140
  Planarity :  0.004   0.047   4525
  Dihedral  :  5.656  51.420   4535
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.61 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  5.23 %
    Favored  : 93.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.03 %
    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: -0.02 (0.15), residues: 3137
  helix:  1.70 (0.21), residues: 649
  sheet:  0.67 (0.18), residues: 715
  loop : -1.00 (0.15), residues: 1773

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 420 
 HIS   0.008   0.001   HIS B 137 
 PHE   0.025   0.002   PHE B 159 
 TYR   0.026   0.002   TYR C 161 
 ARG   0.007   0.001   ARG A 341 

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

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

  6274 Ramachandran restraints generated.
    3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6274 Ramachandran restraints generated.
    3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  321 residues out of total 2771 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 290
  time to evaluate  : 2.900 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.6282 (m-40) cc_final: 0.6062 (m-40)
REVERT: A   90 VAL cc_start: 0.8586 (t) cc_final: 0.8135 (p)
REVERT: A  137 HIS cc_start: 0.4499 (OUTLIER) cc_final: 0.4194 (p-80)
REVERT: A  162 VAL cc_start: 0.8213 (t) cc_final: 0.7804 (p)
REVERT: A  386 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7984 (tp)
REVERT: A  435 TYR cc_start: 0.6802 (m-80) cc_final: 0.6416 (m-80)
REVERT: A  641 ASN cc_start: 0.7481 (t0) cc_final: 0.7140 (t0)
REVERT: A  729 ASP cc_start: 0.7632 (p0) cc_final: 0.7352 (p0)
REVERT: A  842 LEU cc_start: 0.8336 (tp) cc_final: 0.7964 (mt)
REVERT: A 1122 TYR cc_start: 0.7753 (t80) cc_final: 0.7467 (m-10)
REVERT: B   28 TYR cc_start: 0.7346 (m-80) cc_final: 0.7117 (m-80)
REVERT: B  144 MET cc_start: 0.1994 (ttm) cc_final: 0.1447 (tpt)
REVERT: B  917 LYS cc_start: 0.8819 (mttt) cc_final: 0.8585 (mtmm)
REVERT: B  972 GLU cc_start: 0.7157 (mp0) cc_final: 0.6924 (mp0)
REVERT: B 1058 ASN cc_start: 0.7072 (p0) cc_final: 0.6865 (p0)
REVERT: B 1128 GLU cc_start: 0.7424 (tp30) cc_final: 0.7192 (mm-30)
REVERT: C   63 THR cc_start: 0.8007 (m) cc_final: 0.7761 (p)
REVERT: C  120 VAL cc_start: 0.7995 (t) cc_final: 0.7749 (m)
REVERT: C  324 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7175 (tm-30)
REVERT: C  448 PHE cc_start: 0.7928 (m-80) cc_final: 0.7604 (m-80)
REVERT: C  489 TYR cc_start: 0.3018 (OUTLIER) cc_final: 0.1586 (m-80)
REVERT: C  492 TYR cc_start: 0.6697 (m-80) cc_final: 0.6035 (m-10)
REVERT: C  566 LEU cc_start: 0.8078 (mp) cc_final: 0.7817 (mp)
  outliers start: 31
  outliers final: 14
  residues processed: 310
  average time/residue: 0.3851
  time to fit residues: 190.8031
Evaluate side-chains
  229 residues out of total 2771 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 212
  time to evaluate  : 2.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 HIS
Chi-restraints excluded: chain A residue  318 ASN
Chi-restraints excluded: chain A residue  354 ASN
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain B residue   66 HIS
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  222 ILE
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  629 THR
Chi-restraints excluded: chain B residue  840 ASN
Chi-restraints excluded: chain C residue  277 LEU
Chi-restraints excluded: chain C residue  345 CYS
Chi-restraints excluded: chain C residue  369 THR
Chi-restraints excluded: chain C residue  416 CYS
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  729 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 315
   random chunks:
   chunk 158 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   chunk 238 optimal weight:    4.9990
   chunk 194 optimal weight:    4.9990
   chunk 78 optimal weight:    0.7980
   chunk 286 optimal weight:    0.0010
   chunk 309 optimal weight:    2.9990
   chunk 255 optimal weight:    9.9990
   chunk 284 optimal weight:   10.0000
   chunk 97 optimal weight:    0.7980
   chunk 229 optimal weight:    8.9990
   overall best weight:    1.3190

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

Flipped N/Q/H residues before XYZ refinement:
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 137 HIS
A 209 GLN
A 315 ASN
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 701 ASN
A 885 GLN
** A1032 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  66 HIS
B 587 ASN
B 994 GLN
C 125 ASN
C 202 ASN
C 266 ASN
C 639 HIS
** C1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.2775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  26053  Z= 0.228
  Angle     :  0.597  10.706  35484  Z= 0.315
  Chirality :  0.045   0.457   4140
  Planarity :  0.004   0.043   4525
  Dihedral  :  5.600  48.906   4533
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  6.41 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  :  6.78 %
    Favored  : 91.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.03 %
    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: -0.09 (0.15), residues: 3137
  helix:  1.79 (0.21), residues: 655
  sheet:  0.57 (0.18), residues: 732
  loop : -1.11 (0.15), residues: 1750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 617 
 HIS   0.017   0.001   HIS B  66 
 PHE   0.027   0.002   PHE B 159 
 TYR   0.025   0.002   TYR B1051 
 ARG   0.007   0.000   ARG C 181 

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

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

  6274 Ramachandran restraints generated.
    3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6274 Ramachandran restraints generated.
    3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 2771 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 225
  time to evaluate  : 3.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7902 (m-10)
REVERT: A  387 ARG cc_start: 0.6189 (ttt180) cc_final: 0.5502 (mpt180)
REVERT: A  435 TYR cc_start: 0.6851 (m-80) cc_final: 0.6566 (m-80)
REVERT: A  729 ASP cc_start: 0.7565 (p0) cc_final: 0.7224 (p0)
REVERT: A  792 ASP cc_start: 0.5975 (OUTLIER) cc_final: 0.5603 (p0)
REVERT: A  842 LEU cc_start: 0.8415 (tp) cc_final: 0.8009 (mp)
REVERT: A  900 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8451 (tt)
REVERT: B  144 MET cc_start: 0.1811 (ttm) cc_final: 0.1325 (tpt)
REVERT: B 1058 ASN cc_start: 0.7438 (p0) cc_final: 0.7228 (p0)
REVERT: B 1128 GLU cc_start: 0.7416 (tp30) cc_final: 0.7150 (mm-30)
REVERT: C   63 THR cc_start: 0.8041 (m) cc_final: 0.7718 (p)
REVERT: C  120 VAL cc_start: 0.7943 (t) cc_final: 0.7675 (m)
REVERT: C  324 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7179 (tm-30)
REVERT: C  489 TYR cc_start: 0.3248 (OUTLIER) cc_final: 0.1788 (m-80)
REVERT: C  566 LEU cc_start: 0.8038 (mp) cc_final: 0.7816 (mp)
  outliers start: 39
  outliers final: 24
  residues processed: 257
  average time/residue: 0.3538
  time to fit residues: 149.5325
Evaluate side-chains
  217 residues out of total 2771 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 189
  time to evaluate  : 2.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 PHE
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  734 SER
Chi-restraints excluded: chain A residue  792 ASP
Chi-restraints excluded: chain A residue  839 PHE
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  531 THR
Chi-restraints excluded: chain B residue  556 THR
Chi-restraints excluded: chain B residue  629 THR
Chi-restraints excluded: chain B residue  840 ASN
Chi-restraints excluded: chain B residue 1016 CYS
Chi-restraints excluded: chain C residue  125 ASN
Chi-restraints excluded: chain C residue  337 TRP
Chi-restraints excluded: chain C residue  345 CYS
Chi-restraints excluded: chain C residue  348 ASP
Chi-restraints excluded: chain C residue  369 THR
Chi-restraints excluded: chain C residue  376 PHE
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  494 VAL
Chi-restraints excluded: chain C residue  729 ASP
Chi-restraints excluded: chain C residue 1016 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 315
   random chunks:
   chunk 283 optimal weight:    3.9990
   chunk 215 optimal weight:    9.9990
   chunk 148 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 136 optimal weight:    5.9990
   chunk 192 optimal weight:    3.9990
   chunk 287 optimal weight:    1.9990
   chunk 304 optimal weight:    3.9990
   chunk 150 optimal weight:    8.9990
   chunk 272 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 139 ASN
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 701 ASN
** A1032 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 198 HIS
B 639 HIS
B 885 GLN
C1082 ASN
** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.3210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  26053  Z= 0.291
  Angle     :  0.612   9.940  35484  Z= 0.320
  Chirality :  0.046   0.424   4140
  Planarity :  0.004   0.042   4525
  Dihedral  :  5.644  47.912   4533
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.66 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  7.80 %
    Favored  : 90.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.03 %
    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: -0.33 (0.15), residues: 3137
  helix:  1.66 (0.21), residues: 670
  sheet:  0.37 (0.19), residues: 726
  loop : -1.29 (0.15), residues: 1741

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 870 
 HIS   0.006   0.001   HIS B 639 
 PHE   0.023   0.002   PHE C 384 
 TYR   0.024   0.002   TYR B1051 
 ARG   0.005   0.000   ARG C 102 

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

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

  6274 Ramachandran restraints generated.
    3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6274 Ramachandran restraints generated.
    3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 2771 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 41
    poor density    : 203
  time to evaluate  : 3.029 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7998 (m-10)
REVERT: A  168 MET cc_start: 0.6874 (mpp) cc_final: 0.6417 (mpp)
REVERT: A  225 ASN cc_start: 0.6689 (OUTLIER) cc_final: 0.6466 (m-40)
REVERT: A  387 ARG cc_start: 0.6079 (ttt180) cc_final: 0.5375 (mpt180)
REVERT: A  401 LYS cc_start: 0.7544 (mmtp) cc_final: 0.7307 (mmtp)
REVERT: A  435 TYR cc_start: 0.6906 (m-80) cc_final: 0.6631 (m-80)
REVERT: A  446 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7193 (mtpp)
REVERT: A  701 ASN cc_start: 0.9058 (OUTLIER) cc_final: 0.8760 (t0)
REVERT: A  729 ASP cc_start: 0.7619 (p0) cc_final: 0.7294 (p0)
REVERT: B   52 GLN cc_start: 0.7832 (tp40) cc_final: 0.7572 (tp40)
REVERT: B  144 MET cc_start: 0.1829 (ttm) cc_final: 0.1463 (tpt)
REVERT: B 1128 GLU cc_start: 0.7410 (tp30) cc_final: 0.7121 (mm-30)
REVERT: C   63 THR cc_start: 0.8080 (m) cc_final: 0.7668 (p)
REVERT: C  120 VAL cc_start: 0.7918 (t) cc_final: 0.7630 (m)
REVERT: C  324 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7166 (tm-30)
REVERT: C  489 TYR cc_start: 0.3587 (OUTLIER) cc_final: 0.2150 (m-80)
REVERT: C  492 TYR cc_start: 0.6324 (m-80) cc_final: 0.6073 (m-10)
REVERT: C  566 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7987 (mp)
  outliers start: 41
  outliers final: 26
  residues processed: 234
  average time/residue: 0.3327
  time to fit residues: 130.8118
Evaluate side-chains
  209 residues out of total 2771 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 177
  time to evaluate  : 2.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 PHE
Chi-restraints excluded: chain A residue  225 ASN
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  446 LYS
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  629 THR
Chi-restraints excluded: chain A residue  701 ASN
Chi-restraints excluded: chain A residue  734 SER
Chi-restraints excluded: chain A residue  839 PHE
Chi-restraints excluded: chain A residue  952 SER
Chi-restraints excluded: chain A residue 1078 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  556 THR
Chi-restraints excluded: chain B residue  629 THR
Chi-restraints excluded: chain B residue  707 THR
Chi-restraints excluded: chain B residue  840 ASN
Chi-restraints excluded: chain B residue 1016 CYS
Chi-restraints excluded: chain C residue  337 TRP
Chi-restraints excluded: chain C residue  345 CYS
Chi-restraints excluded: chain C residue  348 ASP
Chi-restraints excluded: chain C residue  369 THR
Chi-restraints excluded: chain C residue  416 CYS
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  494 VAL
Chi-restraints excluded: chain C residue  566 LEU
Chi-restraints excluded: chain C residue  729 ASP
Chi-restraints excluded: chain C residue  862 LEU
Chi-restraints excluded: chain C residue 1016 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 315
   random chunks:
   chunk 253 optimal weight:    7.9990
   chunk 172 optimal weight:    0.9990
   chunk 4 optimal weight:    8.9990
   chunk 226 optimal weight:    4.9990
   chunk 125 optimal weight:    6.9990
   chunk 259 optimal weight:    8.9990
   chunk 210 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 155 optimal weight:    7.9990
   chunk 273 optimal weight:    2.9990
   chunk 76 optimal weight:    0.2980
   overall best weight:    3.2588

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

Flipped N/Q/H residues before XYZ refinement:
A 139 ASN
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 639 HIS
A1032 HIS
B 693 ASN
** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 179 ASN
C 597 GLN
C 898 ASN
** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.3683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.076  26053  Z= 0.428
  Angle     :  0.675   9.287  35484  Z= 0.351
  Chirality :  0.049   0.251   4140
  Planarity :  0.005   0.042   4525
  Dihedral  :  6.367  50.465   4533
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.11 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  :  8.52 %
    Favored  : 89.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.03 %
    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: -0.59 (0.15), residues: 3137
  helix:  1.57 (0.21), residues: 654
  sheet:  0.18 (0.19), residues: 684
  loop : -1.44 (0.14), residues: 1799

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 870 
 HIS   0.007   0.001   HIS B1042 
 PHE   0.028   0.002   PHE B 159 
 TYR   0.025   0.002   TYR B1051 
 ARG   0.006   0.001   ARG B 998 

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

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

  6274 Ramachandran restraints generated.
    3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6274 Ramachandran restraints generated.
    3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 2771 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 53
    poor density    : 196
  time to evaluate  : 3.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.8144 (m-10)
REVERT: A  168 MET cc_start: 0.7039 (mpp) cc_final: 0.6439 (mpp)
REVERT: A  387 ARG cc_start: 0.5936 (ttt180) cc_final: 0.5234 (mpt180)
REVERT: A  446 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7439 (mtpp)
REVERT: A  729 ASP cc_start: 0.7712 (p0) cc_final: 0.7334 (p0)
REVERT: B  144 MET cc_start: 0.1605 (ttm) cc_final: 0.1402 (tpt)
REVERT: B 1128 GLU cc_start: 0.7286 (tp30) cc_final: 0.7062 (mm-30)
REVERT: C   63 THR cc_start: 0.8091 (m) cc_final: 0.7625 (p)
REVERT: C  120 VAL cc_start: 0.7961 (t) cc_final: 0.7749 (m)
REVERT: C  489 TYR cc_start: 0.4000 (OUTLIER) cc_final: 0.2430 (m-80)
REVERT: C  492 TYR cc_start: 0.6472 (m-80) cc_final: 0.6107 (m-10)
REVERT: C  566 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.8019 (mp)
  outliers start: 53
  outliers final: 41
  residues processed: 236
  average time/residue: 0.3516
  time to fit residues: 138.7653
Evaluate side-chains
  221 residues out of total 2771 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 176
  time to evaluate  : 2.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 PHE
Chi-restraints excluded: chain A residue  156 ASN
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  318 ASN
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  446 LYS
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  629 THR
Chi-restraints excluded: chain A residue  734 SER
Chi-restraints excluded: chain A residue  839 PHE
Chi-restraints excluded: chain A residue  952 SER
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  222 ILE
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  556 THR
Chi-restraints excluded: chain B residue  587 ASN
Chi-restraints excluded: chain B residue  629 THR
Chi-restraints excluded: chain B residue  840 ASN
Chi-restraints excluded: chain B residue  969 ASP
Chi-restraints excluded: chain B residue 1016 CYS
Chi-restraints excluded: chain B residue 1102 ASP
Chi-restraints excluded: chain C residue   58 PHE
Chi-restraints excluded: chain C residue  179 ASN
Chi-restraints excluded: chain C residue  231 THR
Chi-restraints excluded: chain C residue  345 CYS
Chi-restraints excluded: chain C residue  348 ASP
Chi-restraints excluded: chain C residue  369 THR
Chi-restraints excluded: chain C residue  384 PHE
Chi-restraints excluded: chain C residue  416 CYS
Chi-restraints excluded: chain C residue  454 THR
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  494 VAL
Chi-restraints excluded: chain C residue  566 LEU
Chi-restraints excluded: chain C residue  603 GLU
Chi-restraints excluded: chain C residue  724 MET
Chi-restraints excluded: chain C residue  729 ASP
Chi-restraints excluded: chain C residue  834 ILE
Chi-restraints excluded: chain C residue  885 GLN
Chi-restraints excluded: chain C residue 1016 CYS
Chi-restraints excluded: chain C residue 1082 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 315
   random chunks:
   chunk 102 optimal weight:    0.9980
   chunk 274 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 178 optimal weight:    0.9980
   chunk 75 optimal weight:    0.8980
   chunk 304 optimal weight:    1.9990
   chunk 253 optimal weight:    0.2980
   chunk 141 optimal weight:    4.9990
   chunk 25 optimal weight:    0.8980
   chunk 100 optimal weight:    0.6980
   chunk 160 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 139 ASN
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 338 ASN
C 597 GLN
C 701 ASN
C1085 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.3803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  26053  Z= 0.163
  Angle     :  0.547   9.275  35484  Z= 0.288
  Chirality :  0.044   0.291   4140
  Planarity :  0.004   0.042   4525
  Dihedral  :  5.545  48.608   4533
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.85 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  :  9.49 %
    Favored  : 88.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.03 %
    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: -0.39 (0.15), residues: 3137
  helix:  2.02 (0.21), residues: 646
  sheet:  0.17 (0.19), residues: 707
  loop : -1.37 (0.14), residues: 1784

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 337 
 HIS   0.004   0.001   HIS B 137 
 PHE   0.027   0.001   PHE B 159 
 TYR   0.024   0.001   TYR B 136 
 ARG   0.011   0.000   ARG C 181 

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

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

  6274 Ramachandran restraints generated.
    3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6274 Ramachandran restraints generated.
    3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 2771 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 200
  time to evaluate  : 3.030 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 MET cc_start: 0.6953 (mpp) cc_final: 0.6341 (mpp)
REVERT: A  225 ASN cc_start: 0.6506 (OUTLIER) cc_final: 0.6177 (m-40)
REVERT: A  387 ARG cc_start: 0.6011 (ttt180) cc_final: 0.5097 (mmp-170)
REVERT: A  401 LYS cc_start: 0.7600 (mmtp) cc_final: 0.7377 (mmtp)
REVERT: A  446 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7362 (mtpp)
REVERT: A  505 PRO cc_start: 0.7467 (Cg_endo) cc_final: 0.7226 (Cg_exo)
REVERT: A  729 ASP cc_start: 0.7658 (p0) cc_final: 0.7288 (p0)
REVERT: A  900 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8429 (tt)
REVERT: B   52 GLN cc_start: 0.7757 (tp40) cc_final: 0.7530 (tp40)
REVERT: B 1128 GLU cc_start: 0.7217 (tp30) cc_final: 0.6975 (mm-30)
REVERT: C   63 THR cc_start: 0.7984 (m) cc_final: 0.7655 (p)
REVERT: C  120 VAL cc_start: 0.7939 (t) cc_final: 0.7703 (m)
REVERT: C  448 PHE cc_start: 0.7884 (m-80) cc_final: 0.7572 (m-80)
REVERT: C  489 TYR cc_start: 0.3635 (OUTLIER) cc_final: 0.2119 (m-80)
REVERT: C  492 TYR cc_start: 0.6475 (m-80) cc_final: 0.6184 (m-10)
  outliers start: 43
  outliers final: 24
  residues processed: 235
  average time/residue: 0.3369
  time to fit residues: 129.8729
Evaluate side-chains
  202 residues out of total 2771 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 174
  time to evaluate  : 2.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  225 ASN
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  446 LYS
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  839 PHE
Chi-restraints excluded: chain A residue  840 ASN
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  222 ILE
Chi-restraints excluded: chain B residue  556 THR
Chi-restraints excluded: chain B residue  587 ASN
Chi-restraints excluded: chain B residue  629 THR
Chi-restraints excluded: chain B residue  840 ASN
Chi-restraints excluded: chain B residue 1102 ASP
Chi-restraints excluded: chain C residue  231 THR
Chi-restraints excluded: chain C residue  345 CYS
Chi-restraints excluded: chain C residue  348 ASP
Chi-restraints excluded: chain C residue  369 THR
Chi-restraints excluded: chain C residue  376 PHE
Chi-restraints excluded: chain C residue  384 PHE
Chi-restraints excluded: chain C residue  416 CYS
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  603 GLU
Chi-restraints excluded: chain C residue  701 ASN
Chi-restraints excluded: chain C residue 1016 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 315
   random chunks:
   chunk 293 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9980
   chunk 173 optimal weight:    6.9990
   chunk 222 optimal weight:    3.9990
   chunk 172 optimal weight:    2.9990
   chunk 256 optimal weight:    0.8980
   chunk 170 optimal weight:    3.9990
   chunk 303 optimal weight:    1.9990
   chunk 190 optimal weight:    5.9990
   chunk 185 optimal weight:    2.9990
   chunk 140 optimal weight:    0.9980
   overall best weight:    1.5784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Sorry: Reduce crashed with command 'molprobity.reduce  -quiet -trim -'.
Dumping stdin to file 'reduce_failure.pdb'.
Return code: -15
Dumping stderr: