Starting phenix.real_space_refine
on Mon Dec 30 12:26:35 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vsz_43512/12_2024/8vsz_43512.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vsz_43512/12_2024/8vsz_43512.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vsz_43512/12_2024/8vsz_43512.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vsz_43512/12_2024/8vsz_43512.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vsz_43512/12_2024/8vsz_43512.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vsz_43512/12_2024/8vsz_43512.cif"
  }
  resolution = 3.07
  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=   0.004 sd=   0.039
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      65      5.16       5
     C    8590      2.51       5
     N    2100      2.21       5
     O    2465      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 13220
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2580
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2580
          Classifications: {'peptide': 316}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 307}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Restraints were copied for chains:
    C, B, E, D, F, I, H, J
  Time building chain proxies: 6.10, per 1000 atoms: 0.46
  Number of scatterers: 13220
  At special positions: 0
  Unit cell: (93.225, 91.575, 120.45, 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      65     16.00
     O    2465      8.00
     N    2100      7.00
     C    8590      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 160 " - pdb=" SG  CYS A 174 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 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=5, symmetry=0
  Links applied
    ALPHA1-4
      " BMA F   3 " - " MAN F   4 "
      " BMA G   3 " - " MAN G   4 "
      " BMA H   3 " - " MAN H   4 "
      " BMA I   3 " - " MAN I   4 "
      " BMA J   3 " - " MAN J   4 "
    BETA1-4
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
      " NAG H   1 " - " NAG H   2 "
      " NAG H   2 " - " BMA H   3 "
      " NAG I   1 " - " NAG I   2 "
      " NAG I   2 " - " BMA I   3 "
      " NAG J   1 " - " NAG J   2 "
      " NAG J   2 " - " BMA J   3 "
    NAG-ASN
      " NAG A 501 " - " ASN A 196 "
      " NAG B 501 " - " ASN B 196 "
      " NAG C 501 " - " ASN C 196 "
      " NAG D 501 " - " ASN D 196 "
      " NAG E 501 " - " ASN E 196 "
      " NAG F   1 " - " ASN A 145 "
      " NAG G   1 " - " ASN B 145 "
      " NAG H   1 " - " ASN C 145 "
      " NAG I   1 " - " ASN D 145 "
      " NAG J   1 " - " ASN E 145 "
  Number of additional bonds: simple=5, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.64
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3010

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 20 sheets defined
      36.4% alpha, 43.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.68
  Creating SS restraints...
    Processing helix  chain 'A' and resid 194 through 197
    Processing helix  chain 'A' and resid 201 through 205
    Processing helix  chain 'A' and resid 241 through 249
      removed outlier: 4.050A  pdb=" N   PHE A 245 " --> pdb=" O   ASN A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 263
    Processing helix  chain 'A' and resid 264 through 266
      No H-bonds generated for 'chain 'A' and resid 264 through 266'
    Processing helix  chain 'A' and resid 270 through 296
      removed outlier: 3.684A  pdb=" N   LEU A 296 " --> pdb=" O   SER A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 332
      removed outlier: 3.609A  pdb=" N   VAL A 308 " --> pdb=" O   LYS A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 420
      removed outlier: 4.334A  pdb=" N   LEU A 420 " --> pdb=" O   HIS A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 437
    Processing helix  chain 'B' and resid 194 through 197
    Processing helix  chain 'B' and resid 201 through 205
    Processing helix  chain 'B' and resid 241 through 249
      removed outlier: 4.050A  pdb=" N   PHE B 245 " --> pdb=" O   ASN B 241 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 263
    Processing helix  chain 'B' and resid 264 through 266
      No H-bonds generated for 'chain 'B' and resid 264 through 266'
    Processing helix  chain 'B' and resid 270 through 296
      removed outlier: 3.684A  pdb=" N   LEU B 296 " --> pdb=" O   SER B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 332
      removed outlier: 3.608A  pdb=" N   VAL B 308 " --> pdb=" O   LYS B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 415 through 420
      removed outlier: 4.334A  pdb=" N   LEU B 420 " --> pdb=" O   HIS B 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 437
    Processing helix  chain 'C' and resid 194 through 197
    Processing helix  chain 'C' and resid 201 through 205
    Processing helix  chain 'C' and resid 241 through 249
      removed outlier: 4.049A  pdb=" N   PHE C 245 " --> pdb=" O   ASN C 241 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 249 through 263
    Processing helix  chain 'C' and resid 264 through 266
      No H-bonds generated for 'chain 'C' and resid 264 through 266'
    Processing helix  chain 'C' and resid 270 through 296
      removed outlier: 3.684A  pdb=" N   LEU C 296 " --> pdb=" O   SER C 292 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 304 through 332
      removed outlier: 3.608A  pdb=" N   VAL C 308 " --> pdb=" O   LYS C 304 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 415 through 420
      removed outlier: 4.334A  pdb=" N   LEU C 420 " --> pdb=" O   HIS C 416 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 421 through 437
    Processing helix  chain 'D' and resid 194 through 197
    Processing helix  chain 'D' and resid 201 through 205
    Processing helix  chain 'D' and resid 241 through 249
      removed outlier: 4.050A  pdb=" N   PHE D 245 " --> pdb=" O   ASN D 241 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 249 through 263
    Processing helix  chain 'D' and resid 264 through 266
      No H-bonds generated for 'chain 'D' and resid 264 through 266'
    Processing helix  chain 'D' and resid 270 through 296
      removed outlier: 3.684A  pdb=" N   LEU D 296 " --> pdb=" O   SER D 292 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 304 through 332
      removed outlier: 3.608A  pdb=" N   VAL D 308 " --> pdb=" O   LYS D 304 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 415 through 420
      removed outlier: 4.334A  pdb=" N   LEU D 420 " --> pdb=" O   HIS D 416 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 421 through 437
    Processing helix  chain 'E' and resid 194 through 197
    Processing helix  chain 'E' and resid 201 through 205
    Processing helix  chain 'E' and resid 241 through 249
      removed outlier: 4.050A  pdb=" N   PHE E 245 " --> pdb=" O   ASN E 241 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 249 through 263
    Processing helix  chain 'E' and resid 264 through 266
      No H-bonds generated for 'chain 'E' and resid 264 through 266'
    Processing helix  chain 'E' and resid 270 through 296
      removed outlier: 3.684A  pdb=" N   LEU E 296 " --> pdb=" O   SER E 292 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 304 through 332
      removed outlier: 3.608A  pdb=" N   VAL E 308 " --> pdb=" O   LYS E 304 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 415 through 420
      removed outlier: 4.333A  pdb=" N   LEU E 420 " --> pdb=" O   HIS E 416 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 421 through 437
    Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 107
      removed outlier: 3.790A  pdb=" N   ILE A 140 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   ASP A  81 " --> pdb=" O   SER A  74 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   SER A  74 " --> pdb=" O   ASP A  81 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   THR A  83 " --> pdb=" O   ILE A  72 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ILE A  72 " --> pdb=" O   THR A  83 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   THR A  85 " --> pdb=" O   ALA A  70 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   MET A  93 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   GLN A  62 " --> pdb=" O   MET A  93 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 130
      removed outlier: 6.939A  pdb=" N   THR A 157 " --> pdb=" O   LYS A 126 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   SER A 128 " --> pdb=" O   THR A 155 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   THR A 155 " --> pdb=" O   SER A 128 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   LEU A 130 " --> pdb=" O   ARG A 153 " (cutoff:3.500A)
      removed outlier: 7.461A  pdb=" N   ARG A 153 " --> pdb=" O   LEU A 130 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   ASP A  81 " --> pdb=" O   SER A  74 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   SER A  74 " --> pdb=" O   ASP A  81 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   THR A  83 " --> pdb=" O   ILE A  72 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ILE A  72 " --> pdb=" O   THR A  83 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   THR A  85 " --> pdb=" O   ALA A  70 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   MET A  93 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   GLN A  62 " --> pdb=" O   MET A  93 " (cutoff:3.500A)
      removed outlier: 8.665A  pdb=" N   ARG A 200 " --> pdb=" O   LEU A  65 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   LEU A  67 " --> pdb=" O   ARG A 200 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 122
    Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 122
    Processing sheet with id=AA5, first strand: chain 'B' and resid 105 through 107
      removed outlier: 3.790A  pdb=" N   ILE B 140 " --> pdb=" O   LEU B 107 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   ASP B  81 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   SER B  74 " --> pdb=" O   ASP B  81 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   THR B  83 " --> pdb=" O   ILE B  72 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ILE B  72 " --> pdb=" O   THR B  83 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   THR B  85 " --> pdb=" O   ALA B  70 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   MET B  93 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   GLN B  62 " --> pdb=" O   MET B  93 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 130
      removed outlier: 6.939A  pdb=" N   THR B 157 " --> pdb=" O   LYS B 126 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   SER B 128 " --> pdb=" O   THR B 155 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   THR B 155 " --> pdb=" O   SER B 128 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   LEU B 130 " --> pdb=" O   ARG B 153 " (cutoff:3.500A)
      removed outlier: 7.461A  pdb=" N   ARG B 153 " --> pdb=" O   LEU B 130 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   ASP B  81 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   SER B  74 " --> pdb=" O   ASP B  81 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   THR B  83 " --> pdb=" O   ILE B  72 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ILE B  72 " --> pdb=" O   THR B  83 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   THR B  85 " --> pdb=" O   ALA B  70 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   MET B  93 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   GLN B  62 " --> pdb=" O   MET B  93 " (cutoff:3.500A)
      removed outlier: 8.665A  pdb=" N   ARG B 200 " --> pdb=" O   LEU B  65 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   LEU B  67 " --> pdb=" O   ARG B 200 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 120 through 122
    Processing sheet with id=AA8, first strand: chain 'B' and resid 120 through 122
    Processing sheet with id=AA9, first strand: chain 'C' and resid 105 through 107
      removed outlier: 3.790A  pdb=" N   ILE C 140 " --> pdb=" O   LEU C 107 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   ASP C  81 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   SER C  74 " --> pdb=" O   ASP C  81 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   THR C  83 " --> pdb=" O   ILE C  72 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ILE C  72 " --> pdb=" O   THR C  83 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   THR C  85 " --> pdb=" O   ALA C  70 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   MET C  93 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   GLN C  62 " --> pdb=" O   MET C  93 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 125 through 130
      removed outlier: 6.939A  pdb=" N   THR C 157 " --> pdb=" O   LYS C 126 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   SER C 128 " --> pdb=" O   THR C 155 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   THR C 155 " --> pdb=" O   SER C 128 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   LEU C 130 " --> pdb=" O   ARG C 153 " (cutoff:3.500A)
      removed outlier: 7.462A  pdb=" N   ARG C 153 " --> pdb=" O   LEU C 130 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   ASP C  81 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   SER C  74 " --> pdb=" O   ASP C  81 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   THR C  83 " --> pdb=" O   ILE C  72 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ILE C  72 " --> pdb=" O   THR C  83 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   THR C  85 " --> pdb=" O   ALA C  70 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   MET C  93 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   GLN C  62 " --> pdb=" O   MET C  93 " (cutoff:3.500A)
      removed outlier: 8.665A  pdb=" N   ARG C 200 " --> pdb=" O   LEU C  65 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   LEU C  67 " --> pdb=" O   ARG C 200 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 120 through 122
    Processing sheet with id=AB3, first strand: chain 'C' and resid 120 through 122
    Processing sheet with id=AB4, first strand: chain 'D' and resid 105 through 107
      removed outlier: 3.790A  pdb=" N   ILE D 140 " --> pdb=" O   LEU D 107 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   ASP D  81 " --> pdb=" O   SER D  74 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   SER D  74 " --> pdb=" O   ASP D  81 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   THR D  83 " --> pdb=" O   ILE D  72 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ILE D  72 " --> pdb=" O   THR D  83 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   THR D  85 " --> pdb=" O   ALA D  70 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   MET D  93 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   GLN D  62 " --> pdb=" O   MET D  93 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 125 through 130
      removed outlier: 6.939A  pdb=" N   THR D 157 " --> pdb=" O   LYS D 126 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   SER D 128 " --> pdb=" O   THR D 155 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   THR D 155 " --> pdb=" O   SER D 128 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   LEU D 130 " --> pdb=" O   ARG D 153 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   ARG D 153 " --> pdb=" O   LEU D 130 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   ASP D  81 " --> pdb=" O   SER D  74 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   SER D  74 " --> pdb=" O   ASP D  81 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   THR D  83 " --> pdb=" O   ILE D  72 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ILE D  72 " --> pdb=" O   THR D  83 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   THR D  85 " --> pdb=" O   ALA D  70 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   MET D  93 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   GLN D  62 " --> pdb=" O   MET D  93 " (cutoff:3.500A)
      removed outlier: 8.665A  pdb=" N   ARG D 200 " --> pdb=" O   LEU D  65 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   LEU D  67 " --> pdb=" O   ARG D 200 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 120 through 122
    Processing sheet with id=AB7, first strand: chain 'D' and resid 120 through 122
    Processing sheet with id=AB8, first strand: chain 'E' and resid 105 through 107
      removed outlier: 3.791A  pdb=" N   ILE E 140 " --> pdb=" O   LEU E 107 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   ASP E  81 " --> pdb=" O   SER E  74 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   SER E  74 " --> pdb=" O   ASP E  81 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   THR E  83 " --> pdb=" O   ILE E  72 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ILE E  72 " --> pdb=" O   THR E  83 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   THR E  85 " --> pdb=" O   ALA E  70 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   MET E  93 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   GLN E  62 " --> pdb=" O   MET E  93 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 125 through 130
      removed outlier: 6.938A  pdb=" N   THR E 157 " --> pdb=" O   LYS E 126 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   SER E 128 " --> pdb=" O   THR E 155 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   THR E 155 " --> pdb=" O   SER E 128 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   LEU E 130 " --> pdb=" O   ARG E 153 " (cutoff:3.500A)
      removed outlier: 7.461A  pdb=" N   ARG E 153 " --> pdb=" O   LEU E 130 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   ASP E  81 " --> pdb=" O   SER E  74 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   SER E  74 " --> pdb=" O   ASP E  81 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   THR E  83 " --> pdb=" O   ILE E  72 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ILE E  72 " --> pdb=" O   THR E  83 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   THR E  85 " --> pdb=" O   ALA E  70 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   MET E  93 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   GLN E  62 " --> pdb=" O   MET E  93 " (cutoff:3.500A)
      removed outlier: 8.665A  pdb=" N   ARG E 200 " --> pdb=" O   LEU E  65 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   LEU E  67 " --> pdb=" O   ARG E 200 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 120 through 122
    Processing sheet with id=AC2, first strand: chain 'E' and resid 120 through 122

    770 hydrogen bonds defined for protein.
    2220 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: 4.36

  Time building geometry restraints manager: 4.13 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3999
        1.34 -     1.46: 3293
        1.46 -     1.58: 6148
        1.58 -     1.69: 0
        1.69 -     1.81: 105
  Bond restraints: 13545
  Sorted by residual:
  bond pdb=" C1  MAN J   4 "
       pdb=" C2  MAN J   4 "
    ideal  model  delta    sigma   weight residual
    1.526  1.558 -0.032 2.00e-02 2.50e+03 2.54e+00
  bond pdb=" C1  MAN I   4 "
       pdb=" C2  MAN I   4 "
    ideal  model  delta    sigma   weight residual
    1.526  1.557 -0.031 2.00e-02 2.50e+03 2.45e+00
  bond pdb=" C1  MAN F   4 "
       pdb=" C2  MAN F   4 "
    ideal  model  delta    sigma   weight residual
    1.526  1.557 -0.031 2.00e-02 2.50e+03 2.43e+00
  bond pdb=" C1  MAN G   4 "
       pdb=" C2  MAN G   4 "
    ideal  model  delta    sigma   weight residual
    1.526  1.557 -0.031 2.00e-02 2.50e+03 2.41e+00
  bond pdb=" C1  MAN H   4 "
       pdb=" C2  MAN H   4 "
    ideal  model  delta    sigma   weight residual
    1.526  1.557 -0.031 2.00e-02 2.50e+03 2.41e+00
  ... (remaining 13540 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 17932
        1.58 -     3.15: 366
        3.15 -     4.73: 87
        4.73 -     6.30: 40
        6.30 -     7.88: 10
  Bond angle restraints: 18435
  Sorted by residual:
  angle pdb=" C   LEU E 420 "
        pdb=" N   LEU E 421 "
        pdb=" CA  LEU E 421 "
      ideal   model   delta    sigma   weight residual
     122.17  115.67    6.50 1.54e+00 4.22e-01 1.78e+01
  angle pdb=" C   LEU B 420 "
        pdb=" N   LEU B 421 "
        pdb=" CA  LEU B 421 "
      ideal   model   delta    sigma   weight residual
     122.17  115.70    6.47 1.54e+00 4.22e-01 1.76e+01
  angle pdb=" C   LEU A 420 "
        pdb=" N   LEU A 421 "
        pdb=" CA  LEU A 421 "
      ideal   model   delta    sigma   weight residual
     122.17  115.71    6.46 1.54e+00 4.22e-01 1.76e+01
  angle pdb=" C   LEU D 420 "
        pdb=" N   LEU D 421 "
        pdb=" CA  LEU D 421 "
      ideal   model   delta    sigma   weight residual
     122.17  115.71    6.46 1.54e+00 4.22e-01 1.76e+01
  angle pdb=" C   LEU C 420 "
        pdb=" N   LEU C 421 "
        pdb=" CA  LEU C 421 "
      ideal   model   delta    sigma   weight residual
     122.17  115.72    6.45 1.54e+00 4.22e-01 1.75e+01
  ... (remaining 18430 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.90: 7084
       21.90 -    43.80: 907
       43.80 -    65.69: 117
       65.69 -    87.59: 45
       87.59 -   109.49: 25
  Dihedral angle restraints: 8178
    sinusoidal: 3498
      harmonic: 4680
  Sorted by residual:
  dihedral pdb=" CB  CYS A 160 "
           pdb=" SG  CYS A 160 "
           pdb=" SG  CYS A 174 "
           pdb=" CB  CYS A 174 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   49.50   43.50     1      1.00e+01 1.00e-02 2.64e+01
  dihedral pdb=" O4  BMA G   3 "
           pdb=" C4  BMA G   3 "
           pdb=" C5  BMA G   3 "
           pdb=" O5  BMA G   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     288.71  179.22  109.49     1      3.00e+01 1.11e-03 1.42e+01
  dihedral pdb=" O4  BMA F   3 "
           pdb=" C4  BMA F   3 "
           pdb=" C5  BMA F   3 "
           pdb=" O5  BMA F   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     288.71  179.24  109.47     1      3.00e+01 1.11e-03 1.42e+01
  ... (remaining 8175 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1871
       0.059 -    0.118: 274
       0.118 -    0.178: 25
       0.178 -    0.237: 5
       0.237 -    0.296: 10
  Chirality restraints: 2185
  Sorted by residual:
  chirality pdb=" C1  NAG C 501 "
            pdb=" ND2 ASN C 196 "
            pdb=" C2  NAG C 501 "
            pdb=" O5  NAG C 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.10   -0.30 2.00e-01 2.50e+01 2.19e+00
  chirality pdb=" C1  NAG D 501 "
            pdb=" ND2 ASN D 196 "
            pdb=" C2  NAG D 501 "
            pdb=" O5  NAG D 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.11   -0.29 2.00e-01 2.50e+01 2.17e+00
  chirality pdb=" C1  NAG A 501 "
            pdb=" ND2 ASN A 196 "
            pdb=" C2  NAG A 501 "
            pdb=" O5  NAG A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.11   -0.29 2.00e-01 2.50e+01 2.17e+00
  ... (remaining 2182 not shown)

  Planarity restraints: 2245
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 261 "    0.007 2.00e-02 2.50e+03   6.16e-03 9.49e-01
        pdb=" CG  TRP B 261 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 261 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 261 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 261 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 261 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 261 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 261 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 261 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 261 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 261 "    0.007 2.00e-02 2.50e+03   6.12e-03 9.36e-01
        pdb=" CG  TRP A 261 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 261 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 261 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 261 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 261 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 261 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 261 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 261 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 261 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 261 "   -0.007 2.00e-02 2.50e+03   6.06e-03 9.18e-01
        pdb=" CG  TRP D 261 "    0.017 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 261 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 261 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 261 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 261 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 261 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 261 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 261 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 261 "    0.000 2.00e-02 2.50e+03
  ... (remaining 2242 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.61: 153
        2.61 -     3.18: 11176
        3.18 -     3.75: 20408
        3.75 -     4.33: 28642
        4.33 -     4.90: 47152
  Nonbonded interactions: 107531
  Sorted by model distance:
  nonbonded pdb=" SG  CYS D 160 "
            pdb=" SG  CYS D 174 "
     model   vdw
     2.032 3.760
  nonbonded pdb=" SG  CYS C 160 "
            pdb=" SG  CYS C 174 "
     model   vdw
     2.032 3.760
  nonbonded pdb=" SG  CYS B 160 "
            pdb=" SG  CYS B 174 "
     model   vdw
     2.033 3.760
  nonbonded pdb=" SG  CYS E 160 "
            pdb=" SG  CYS E 174 "
     model   vdw
     2.033 3.760
  nonbonded pdb=" OG  SER B 180 "
            pdb=" O   TYR B 183 "
     model   vdw
     2.233 3.040
  ... (remaining 107526 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'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

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:             2.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     30.230
  Find NCS groups from input model:        0.570
  Set up NCS constraints:                  0.040
  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:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
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      :  0.003   0.032  13545  Z= 0.202
  Angle     :  0.650   7.879  18435  Z= 0.321
  Chirality :  0.047   0.296   2185
  Planarity :  0.002   0.023   2235
  Dihedral  : 19.650 109.487   5165
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  2.88 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 34.97 %
    Favored  : 65.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.22), residues: 1560
  helix:  2.25 (0.24), residues: 490
  sheet: -1.25 (0.28), residues: 320
  loop : -1.69 (0.22), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 261 
 HIS   0.004   0.001   HIS C 204 
 PHE   0.014   0.001   PHE E 318 
 TYR   0.011   0.001   TYR D 433 
 ARG   0.002   0.000   ARG C  53 

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 1.397 
Fit side-chains
REVERT: B  285 MET cc_start: 0.7070 (tpt) cc_final: 0.6792 (tpt)
REVERT: D  304 LYS cc_start: 0.7626 (mtmm) cc_final: 0.7370 (mtmm)
REVERT: E  304 LYS cc_start: 0.7541 (mtmm) cc_final: 0.7315 (mtmm)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.2381
  time to fit residues: 45.6820
Evaluate side-chains
  118 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 1.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 130 optimal weight:    9.9990
   chunk 117 optimal weight:   20.0000
   chunk 65 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 79 optimal weight:    7.9990
   chunk 62 optimal weight:    2.9990
   chunk 121 optimal weight:   40.0000
   chunk 47 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 90 optimal weight:    5.9990
   chunk 140 optimal weight:    6.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 204 HIS
B 204 HIS
C 204 HIS
D 204 HIS
E 204 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.1411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066  13545  Z= 0.323
  Angle     :  0.686   6.814  18435  Z= 0.342
  Chirality :  0.048   0.335   2185
  Planarity :  0.004   0.027   2235
  Dihedral  : 11.677  80.491   2270
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  3.53 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 32.31 %
    Favored  : 63.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.22), residues: 1560
  helix:  2.48 (0.24), residues: 495
  sheet: -0.99 (0.26), residues: 315
  loop : -1.84 (0.23), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 261 
 HIS   0.005   0.002   HIS B 204 
 PHE   0.023   0.002   PHE D 316 
 TYR   0.016   0.002   TYR E 121 
 ARG   0.003   0.000   ARG B 153 

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 150
  time to evaluate  : 1.446 
Fit side-chains
REVERT: A  234 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8331 (tp)
REVERT: A  318 PHE cc_start: 0.6665 (OUTLIER) cc_final: 0.6067 (p90)
REVERT: C  295 SER cc_start: 0.4060 (OUTLIER) cc_final: 0.3128 (t)
REVERT: C  304 LYS cc_start: 0.7742 (mtmm) cc_final: 0.7403 (mtmt)
REVERT: D  318 PHE cc_start: 0.6365 (OUTLIER) cc_final: 0.6028 (p90)
REVERT: E  304 LYS cc_start: 0.7839 (mtmm) cc_final: 0.7507 (mtmt)
  outliers start: 53
  outliers final: 27
  residues processed: 193
  average time/residue: 0.2196
  time to fit residues: 65.4820
Evaluate side-chains
  158 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 127
  time to evaluate  : 1.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  181 TRP
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain B residue  181 TRP
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  432 PHE
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  211 THR
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  282 VAL
Chi-restraints excluded: chain C residue  295 SER
Chi-restraints excluded: chain C residue  432 PHE
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain D residue  181 TRP
Chi-restraints excluded: chain D residue  211 THR
Chi-restraints excluded: chain D residue  218 LEU
Chi-restraints excluded: chain D residue  234 LEU
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain E residue  140 ILE
Chi-restraints excluded: chain E residue  181 TRP
Chi-restraints excluded: chain E residue  211 THR
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  432 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 78 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9980
   chunk 117 optimal weight:   20.0000
   chunk 95 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 141 optimal weight:    0.8980
   chunk 152 optimal weight:   30.0000
   chunk 125 optimal weight:    0.4980
   chunk 139 optimal weight:    0.3980
   chunk 48 optimal weight:    0.5980
   chunk 113 optimal weight:   10.0000
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 204 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13545  Z= 0.178
  Angle     :  0.609  11.285  18435  Z= 0.296
  Chirality :  0.044   0.278   2185
  Planarity :  0.003   0.024   2235
  Dihedral  : 10.582  70.272   2270
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  2.88 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 31.19 %
    Favored  : 64.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.22), residues: 1560
  helix:  2.53 (0.23), residues: 495
  sheet: -0.98 (0.25), residues: 345
  loop : -1.45 (0.23), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 261 
 HIS   0.004   0.001   HIS A 204 
 PHE   0.020   0.001   PHE B 316 
 TYR   0.012   0.001   TYR D 121 
 ARG   0.002   0.000   ARG E 200 

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 140
  time to evaluate  : 1.420 
Fit side-chains
REVERT: A  247 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7239 (tt)
REVERT: A  295 SER cc_start: 0.3123 (OUTLIER) cc_final: 0.2551 (t)
REVERT: A  318 PHE cc_start: 0.6677 (OUTLIER) cc_final: 0.6075 (p90)
REVERT: B   48 TYR cc_start: 0.0480 (OUTLIER) cc_final: -0.0818 (m-10)
REVERT: B  110 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.6985 (mtm180)
REVERT: B  285 MET cc_start: 0.7161 (tpt) cc_final: 0.6927 (tpt)
REVERT: B  295 SER cc_start: 0.3998 (OUTLIER) cc_final: 0.3229 (t)
REVERT: C  110 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7111 (mtm180)
REVERT: C  250 TYR cc_start: 0.5912 (m-80) cc_final: 0.5675 (m-80)
REVERT: C  304 LYS cc_start: 0.7656 (mtmm) cc_final: 0.7340 (mtmt)
REVERT: D  110 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6953 (mtm180)
REVERT: D  295 SER cc_start: 0.3836 (OUTLIER) cc_final: 0.3105 (t)
REVERT: D  318 PHE cc_start: 0.6372 (OUTLIER) cc_final: 0.6065 (p90)
REVERT: E  110 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6988 (mtt180)
REVERT: E  295 SER cc_start: 0.4216 (OUTLIER) cc_final: 0.3439 (t)
REVERT: E  304 LYS cc_start: 0.7778 (mtmm) cc_final: 0.7433 (mtmt)
  outliers start: 66
  outliers final: 32
  residues processed: 193
  average time/residue: 0.2729
  time to fit residues: 75.5345
Evaluate side-chains
  178 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 134
  time to evaluate  : 1.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  181 TRP
Chi-restraints excluded: chain A residue  215 TYR
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue   48 TYR
Chi-restraints excluded: chain B residue  110 ARG
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  181 TRP
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  295 SER
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain B residue  432 PHE
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue  104 SER
Chi-restraints excluded: chain C residue  110 ARG
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  215 TYR
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  306 ILE
Chi-restraints excluded: chain C residue  316 PHE
Chi-restraints excluded: chain C residue  432 PHE
Chi-restraints excluded: chain D residue  110 ARG
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  181 TRP
Chi-restraints excluded: chain D residue  215 TYR
Chi-restraints excluded: chain D residue  234 LEU
Chi-restraints excluded: chain D residue  295 SER
Chi-restraints excluded: chain D residue  306 ILE
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain E residue  110 ARG
Chi-restraints excluded: chain E residue  128 SER
Chi-restraints excluded: chain E residue  181 TRP
Chi-restraints excluded: chain E residue  215 TYR
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain E residue  295 SER
Chi-restraints excluded: chain E residue  316 PHE
Chi-restraints excluded: chain E residue  432 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 139 optimal weight:    3.9990
   chunk 106 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 67 optimal weight:    9.9990
   chunk 94 optimal weight:    0.8980
   chunk 141 optimal weight:    0.9980
   chunk 149 optimal weight:    0.9980
   chunk 134 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 124 optimal weight:    7.9990
   overall best weight:    1.7784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.2104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  13545  Z= 0.308
  Angle     :  0.695  10.808  18435  Z= 0.336
  Chirality :  0.047   0.273   2185
  Planarity :  0.004   0.025   2235
  Dihedral  :  9.847  61.298   2270
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  4.17 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  6.57 %
    Allowed  : 30.35 %
    Favored  : 63.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.22), residues: 1560
  helix:  2.52 (0.24), residues: 500
  sheet: -0.91 (0.25), residues: 340
  loop : -1.57 (0.23), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 261 
 HIS   0.004   0.001   HIS D 131 
 PHE   0.018   0.002   PHE C 316 
 TYR   0.012   0.002   TYR B 309 
 ARG   0.003   0.000   ARG A 138 

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 94
    poor density    : 140
  time to evaluate  : 1.429 
Fit side-chains
REVERT: A   48 TYR cc_start: 0.0342 (OUTLIER) cc_final: -0.1943 (m-80)
REVERT: A  234 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8363 (tp)
REVERT: A  318 PHE cc_start: 0.6767 (OUTLIER) cc_final: 0.6137 (p90)
REVERT: B   48 TYR cc_start: 0.0603 (OUTLIER) cc_final: -0.0864 (m-10)
REVERT: B  110 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.7138 (mtm180)
REVERT: B  255 PHE cc_start: 0.5544 (OUTLIER) cc_final: 0.4963 (m-80)
REVERT: B  304 LYS cc_start: 0.7619 (mtmm) cc_final: 0.7235 (mtmt)
REVERT: C   48 TYR cc_start: 0.0590 (OUTLIER) cc_final: -0.2091 (m-80)
REVERT: C  110 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7238 (mtm180)
REVERT: C  255 PHE cc_start: 0.5444 (OUTLIER) cc_final: 0.4858 (m-80)
REVERT: C  304 LYS cc_start: 0.7678 (mtmm) cc_final: 0.7322 (mtmt)
REVERT: D   48 TYR cc_start: 0.0612 (OUTLIER) cc_final: -0.0571 (m-10)
REVERT: D  110 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7066 (mtm180)
REVERT: D  155 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8434 (m)
REVERT: D  255 PHE cc_start: 0.5758 (OUTLIER) cc_final: 0.5158 (m-80)
REVERT: D  318 PHE cc_start: 0.6414 (OUTLIER) cc_final: 0.6082 (p90)
REVERT: E   48 TYR cc_start: 0.0324 (OUTLIER) cc_final: -0.2411 (m-80)
REVERT: E  110 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7180 (mtt180)
REVERT: E  304 LYS cc_start: 0.7785 (mtmm) cc_final: 0.7427 (mtmt)
  outliers start: 94
  outliers final: 47
  residues processed: 217
  average time/residue: 0.2986
  time to fit residues: 91.1280
Evaluate side-chains
  199 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 136
  time to evaluate  : 1.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  181 TRP
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue   48 TYR
Chi-restraints excluded: chain B residue  110 ARG
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain B residue  181 TRP
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain B residue  432 PHE
Chi-restraints excluded: chain C residue   48 TYR
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue  104 SER
Chi-restraints excluded: chain C residue  110 ARG
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  142 LEU
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  211 THR
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  255 PHE
Chi-restraints excluded: chain C residue  306 ILE
Chi-restraints excluded: chain C residue  316 PHE
Chi-restraints excluded: chain C residue  432 PHE
Chi-restraints excluded: chain D residue   48 TYR
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain D residue  110 ARG
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  155 THR
Chi-restraints excluded: chain D residue  181 TRP
Chi-restraints excluded: chain D residue  211 THR
Chi-restraints excluded: chain D residue  218 LEU
Chi-restraints excluded: chain D residue  234 LEU
Chi-restraints excluded: chain D residue  255 PHE
Chi-restraints excluded: chain D residue  306 ILE
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain E residue   48 TYR
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue  104 SER
Chi-restraints excluded: chain E residue  110 ARG
Chi-restraints excluded: chain E residue  128 SER
Chi-restraints excluded: chain E residue  181 TRP
Chi-restraints excluded: chain E residue  211 THR
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  316 PHE
Chi-restraints excluded: chain E residue  432 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 85 optimal weight:   20.0000
   chunk 2 optimal weight:    1.9990
   chunk 111 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 127 optimal weight:    0.9980
   chunk 103 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 76 optimal weight:    3.9990
   chunk 134 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   overall best weight:    1.3584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13545  Z= 0.245
  Angle     :  0.673  11.136  18435  Z= 0.322
  Chirality :  0.046   0.253   2185
  Planarity :  0.003   0.026   2235
  Dihedral  :  9.392  57.249   2270
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  3.33 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  6.36 %
    Allowed  : 30.70 %
    Favored  : 62.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.22), residues: 1560
  helix:  2.56 (0.24), residues: 500
  sheet: -0.85 (0.25), residues: 340
  loop : -1.53 (0.24), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 261 
 HIS   0.004   0.001   HIS B 131 
 PHE   0.025   0.002   PHE A 426 
 TYR   0.012   0.001   TYR C 433 
 ARG   0.006   0.001   ARG A  91 

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 91
    poor density    : 153
  time to evaluate  : 1.444 
Fit side-chains
REVERT: A   48 TYR cc_start: 0.0340 (OUTLIER) cc_final: -0.1916 (m-80)
REVERT: A  155 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8446 (m)
REVERT: A  234 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8306 (tp)
REVERT: A  318 PHE cc_start: 0.6686 (OUTLIER) cc_final: 0.6068 (p90)
REVERT: B   48 TYR cc_start: 0.0566 (OUTLIER) cc_final: -0.0864 (m-10)
REVERT: B  110 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.7118 (mtm180)
REVERT: B  255 PHE cc_start: 0.5589 (OUTLIER) cc_final: 0.4882 (m-80)
REVERT: B  304 LYS cc_start: 0.7635 (mtmm) cc_final: 0.7248 (mtmt)
REVERT: C   48 TYR cc_start: 0.0692 (OUTLIER) cc_final: -0.2000 (m-80)
REVERT: C  110 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7365 (mtm180)
REVERT: C  255 PHE cc_start: 0.5468 (OUTLIER) cc_final: 0.4867 (m-80)
REVERT: C  304 LYS cc_start: 0.7698 (mtmm) cc_final: 0.7289 (mtmt)
REVERT: D   48 TYR cc_start: 0.0642 (OUTLIER) cc_final: -0.0685 (m-10)
REVERT: D  110 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7053 (mtm180)
REVERT: D  155 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8447 (m)
REVERT: D  255 PHE cc_start: 0.5857 (OUTLIER) cc_final: 0.5056 (m-80)
REVERT: D  318 PHE cc_start: 0.6403 (OUTLIER) cc_final: 0.6089 (p90)
REVERT: E   48 TYR cc_start: 0.0390 (OUTLIER) cc_final: -0.2343 (m-80)
REVERT: E  110 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7123 (mtt180)
REVERT: E  304 LYS cc_start: 0.7805 (mtmm) cc_final: 0.7598 (mtmm)
  outliers start: 91
  outliers final: 54
  residues processed: 224
  average time/residue: 0.2443
  time to fit residues: 81.1522
Evaluate side-chains
  208 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 137
  time to evaluate  : 1.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   68 ASP
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  110 ARG
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  161 ASN
Chi-restraints excluded: chain A residue  181 TRP
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  215 TYR
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue   48 TYR
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  110 ARG
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  181 TRP
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain B residue  432 PHE
Chi-restraints excluded: chain C residue   48 TYR
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue  104 SER
Chi-restraints excluded: chain C residue  110 ARG
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  211 THR
Chi-restraints excluded: chain C residue  215 TYR
Chi-restraints excluded: chain C residue  255 PHE
Chi-restraints excluded: chain C residue  306 ILE
Chi-restraints excluded: chain C residue  316 PHE
Chi-restraints excluded: chain C residue  432 PHE
Chi-restraints excluded: chain D residue   48 TYR
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain D residue  110 ARG
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  155 THR
Chi-restraints excluded: chain D residue  181 TRP
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  215 TYR
Chi-restraints excluded: chain D residue  234 LEU
Chi-restraints excluded: chain D residue  255 PHE
Chi-restraints excluded: chain D residue  306 ILE
Chi-restraints excluded: chain D residue  316 PHE
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain E residue   48 TYR
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue  104 SER
Chi-restraints excluded: chain E residue  110 ARG
Chi-restraints excluded: chain E residue  128 SER
Chi-restraints excluded: chain E residue  181 TRP
Chi-restraints excluded: chain E residue  205 LEU
Chi-restraints excluded: chain E residue  211 THR
Chi-restraints excluded: chain E residue  316 PHE
Chi-restraints excluded: chain E residue  432 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 134 optimal weight:    0.6980
   chunk 29 optimal weight:   20.0000
   chunk 87 optimal weight:    6.9990
   chunk 36 optimal weight:    5.9990
   chunk 149 optimal weight:    8.9990
   chunk 124 optimal weight:    0.0010
   chunk 69 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 144 optimal weight:    4.9990
   overall best weight:    1.9392

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

Flipped N/Q/H residues before XYZ refinement:
** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.2659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  13545  Z= 0.322
  Angle     :  0.717  11.039  18435  Z= 0.345
  Chirality :  0.047   0.252   2185
  Planarity :  0.004   0.028   2235
  Dihedral  :  9.082  54.033   2270
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  4.55 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  6.29 %
    Allowed  : 31.05 %
    Favored  : 62.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.22), residues: 1560
  helix:  2.55 (0.24), residues: 500
  sheet: -0.84 (0.24), residues: 335
  loop : -1.69 (0.23), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP E 261 
 HIS   0.005   0.001   HIS B 131 
 PHE   0.029   0.002   PHE B  99 
 TYR   0.011   0.002   TYR A 309 
 ARG   0.006   0.000   ARG E  91 

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 90
    poor density    : 141
  time to evaluate  : 1.410 
Fit side-chains
REVERT: A   48 TYR cc_start: 0.0395 (OUTLIER) cc_final: -0.1836 (m-80)
REVERT: A  155 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8449 (m)
REVERT: A  234 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8323 (tp)
REVERT: A  318 PHE cc_start: 0.6770 (OUTLIER) cc_final: 0.6147 (p90)
REVERT: B   48 TYR cc_start: 0.0540 (OUTLIER) cc_final: -0.0981 (m-10)
REVERT: B  102 ASN cc_start: 0.5726 (p0) cc_final: 0.5484 (p0)
REVERT: B  110 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7248 (mtm180)
REVERT: B  304 LYS cc_start: 0.7651 (mtmm) cc_final: 0.7242 (mtmt)
REVERT: C   48 TYR cc_start: 0.0748 (OUTLIER) cc_final: -0.1921 (m-80)
REVERT: C  102 ASN cc_start: 0.5756 (p0) cc_final: 0.5484 (p0)
REVERT: C  110 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7358 (mtm180)
REVERT: C  255 PHE cc_start: 0.5543 (OUTLIER) cc_final: 0.4833 (m-80)
REVERT: C  304 LYS cc_start: 0.7648 (mtmm) cc_final: 0.7285 (mtmt)
REVERT: D   48 TYR cc_start: 0.0636 (OUTLIER) cc_final: -0.0692 (m-10)
REVERT: D  102 ASN cc_start: 0.5737 (p0) cc_final: 0.5526 (p0)
REVERT: D  110 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7177 (mtm180)
REVERT: D  155 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8452 (m)
REVERT: D  318 PHE cc_start: 0.6522 (OUTLIER) cc_final: 0.6223 (p90)
REVERT: E   48 TYR cc_start: 0.0409 (OUTLIER) cc_final: -0.0982 (m-10)
REVERT: E  110 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7247 (mtt180)
REVERT: E  255 PHE cc_start: 0.5718 (OUTLIER) cc_final: 0.4767 (m-80)
  outliers start: 90
  outliers final: 63
  residues processed: 213
  average time/residue: 0.2435
  time to fit residues: 76.4355
Evaluate side-chains
  211 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 132
  time to evaluate  : 1.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   68 ASP
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  161 ASN
Chi-restraints excluded: chain A residue  181 TRP
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue   48 TYR
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  110 ARG
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain B residue  181 TRP
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain B residue  432 PHE
Chi-restraints excluded: chain C residue   48 TYR
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue   68 ASP
Chi-restraints excluded: chain C residue  104 SER
Chi-restraints excluded: chain C residue  110 ARG
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  211 THR
Chi-restraints excluded: chain C residue  255 PHE
Chi-restraints excluded: chain C residue  306 ILE
Chi-restraints excluded: chain C residue  316 PHE
Chi-restraints excluded: chain C residue  432 PHE
Chi-restraints excluded: chain D residue   48 TYR
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain D residue  110 ARG
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  155 THR
Chi-restraints excluded: chain D residue  161 ASN
Chi-restraints excluded: chain D residue  181 TRP
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  211 THR
Chi-restraints excluded: chain D residue  218 LEU
Chi-restraints excluded: chain D residue  220 THR
Chi-restraints excluded: chain D residue  234 LEU
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  306 ILE
Chi-restraints excluded: chain D residue  312 ILE
Chi-restraints excluded: chain D residue  316 PHE
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain E residue   48 TYR
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue  104 SER
Chi-restraints excluded: chain E residue  110 ARG
Chi-restraints excluded: chain E residue  128 SER
Chi-restraints excluded: chain E residue  140 ILE
Chi-restraints excluded: chain E residue  161 ASN
Chi-restraints excluded: chain E residue  181 TRP
Chi-restraints excluded: chain E residue  205 LEU
Chi-restraints excluded: chain E residue  211 THR
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  220 THR
Chi-restraints excluded: chain E residue  255 PHE
Chi-restraints excluded: chain E residue  316 PHE
Chi-restraints excluded: chain E residue  432 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 85 optimal weight:   20.0000
   chunk 109 optimal weight:    0.1980
   chunk 84 optimal weight:    0.0670
   chunk 126 optimal weight:    0.5980
   chunk 83 optimal weight:    5.9990
   chunk 149 optimal weight:    2.9990
   chunk 93 optimal weight:    9.9990
   chunk 91 optimal weight:    6.9990
   chunk 68 optimal weight:    9.9990
   chunk 92 optimal weight:    2.9990
   overall best weight:    1.3722

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

Flipped N/Q/H residues before XYZ refinement:
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 204 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.2715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13545  Z= 0.250
  Angle     :  0.675  11.089  18435  Z= 0.325
  Chirality :  0.046   0.243   2185
  Planarity :  0.003   0.028   2235
  Dihedral  :  8.677  51.653   2270
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  3.59 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 31.33 %
    Favored  : 62.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.22), residues: 1560
  helix:  2.59 (0.24), residues: 500
  sheet: -0.73 (0.25), residues: 335
  loop : -1.63 (0.23), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D 261 
 HIS   0.005   0.001   HIS E 204 
 PHE   0.027   0.002   PHE B  99 
 TYR   0.013   0.001   TYR C 433 
 ARG   0.005   0.000   ARG E  91 

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 140
  time to evaluate  : 1.259 
Fit side-chains
REVERT: A   48 TYR cc_start: 0.0352 (OUTLIER) cc_final: -0.1741 (m-80)
REVERT: A  102 ASN cc_start: 0.5897 (p0) cc_final: 0.5630 (p0)
REVERT: A  155 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8459 (m)
REVERT: A  234 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8299 (tp)
REVERT: A  318 PHE cc_start: 0.6703 (OUTLIER) cc_final: 0.6186 (p90)
REVERT: B   48 TYR cc_start: 0.0539 (OUTLIER) cc_final: -0.0985 (m-10)
REVERT: B  102 ASN cc_start: 0.5697 (p0) cc_final: 0.5436 (p0)
REVERT: B  110 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7219 (mtm180)
REVERT: B  304 LYS cc_start: 0.7654 (mtmm) cc_final: 0.7233 (mtmt)
REVERT: C   48 TYR cc_start: 0.0751 (OUTLIER) cc_final: -0.1962 (m-80)
REVERT: C  102 ASN cc_start: 0.5789 (p0) cc_final: 0.5549 (p0)
REVERT: C  110 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7333 (mtm180)
REVERT: D   48 TYR cc_start: 0.0661 (OUTLIER) cc_final: -0.0841 (m-10)
REVERT: D  102 ASN cc_start: 0.5669 (p0) cc_final: 0.5458 (p0)
REVERT: D  110 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7189 (mtm180)
REVERT: D  155 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8450 (m)
REVERT: D  255 PHE cc_start: 0.6021 (OUTLIER) cc_final: 0.5586 (m-80)
REVERT: D  318 PHE cc_start: 0.6507 (OUTLIER) cc_final: 0.6126 (p90)
REVERT: E   48 TYR cc_start: 0.0455 (OUTLIER) cc_final: -0.1223 (m-80)
REVERT: E  110 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7202 (mtt180)
REVERT: E  255 PHE cc_start: 0.5848 (OUTLIER) cc_final: 0.4994 (m-80)
  outliers start: 86
  outliers final: 56
  residues processed: 207
  average time/residue: 0.2384
  time to fit residues: 73.2996
Evaluate side-chains
  206 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 134
  time to evaluate  : 1.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  161 ASN
Chi-restraints excluded: chain A residue  181 TRP
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  215 TYR
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue   48 TYR
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  110 ARG
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  181 TRP
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain B residue  432 PHE
Chi-restraints excluded: chain C residue   48 TYR
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue   68 ASP
Chi-restraints excluded: chain C residue  104 SER
Chi-restraints excluded: chain C residue  110 ARG
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  215 TYR
Chi-restraints excluded: chain C residue  316 PHE
Chi-restraints excluded: chain C residue  432 PHE
Chi-restraints excluded: chain D residue   48 TYR
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain D residue  110 ARG
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  155 THR
Chi-restraints excluded: chain D residue  161 ASN
Chi-restraints excluded: chain D residue  181 TRP
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  215 TYR
Chi-restraints excluded: chain D residue  218 LEU
Chi-restraints excluded: chain D residue  234 LEU
Chi-restraints excluded: chain D residue  255 PHE
Chi-restraints excluded: chain D residue  312 ILE
Chi-restraints excluded: chain D residue  316 PHE
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain E residue   48 TYR
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue  104 SER
Chi-restraints excluded: chain E residue  110 ARG
Chi-restraints excluded: chain E residue  128 SER
Chi-restraints excluded: chain E residue  140 ILE
Chi-restraints excluded: chain E residue  181 TRP
Chi-restraints excluded: chain E residue  205 LEU
Chi-restraints excluded: chain E residue  211 THR
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  220 THR
Chi-restraints excluded: chain E residue  255 PHE
Chi-restraints excluded: chain E residue  316 PHE
Chi-restraints excluded: chain E residue  432 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 59 optimal weight:   30.0000
   chunk 89 optimal weight:    8.9990
   chunk 45 optimal weight:    3.9990
   chunk 29 optimal weight:   20.0000
   chunk 28 optimal weight:   50.0000
   chunk 94 optimal weight:    0.9990
   chunk 101 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 117 optimal weight:    6.9990
   chunk 135 optimal weight:    2.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 204 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.3020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  13545  Z= 0.370
  Angle     :  0.747  11.029  18435  Z= 0.361
  Chirality :  0.049   0.251   2185
  Planarity :  0.004   0.031   2235
  Dihedral  :  8.632  48.389   2270
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  4.62 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  6.57 %
    Allowed  : 30.63 %
    Favored  : 62.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.22), residues: 1560
  helix:  2.48 (0.24), residues: 500
  sheet: -0.72 (0.25), residues: 310
  loop : -1.94 (0.23), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D 261 
 HIS   0.004   0.001   HIS E 204 
 PHE   0.031   0.002   PHE B  99 
 TYR   0.011   0.002   TYR B 309 
 ARG   0.008   0.001   ARG B 293 

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 94
    poor density    : 137
  time to evaluate  : 1.457 
Fit side-chains
REVERT: A   48 TYR cc_start: 0.0403 (OUTLIER) cc_final: -0.1604 (m-80)
REVERT: A  102 ASN cc_start: 0.5942 (p0) cc_final: 0.5688 (p0)
REVERT: A  155 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8444 (m)
REVERT: A  234 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8350 (tp)
REVERT: A  318 PHE cc_start: 0.6807 (OUTLIER) cc_final: 0.6368 (p90)
REVERT: B   48 TYR cc_start: 0.0505 (OUTLIER) cc_final: -0.1289 (m-80)
REVERT: B  102 ASN cc_start: 0.5796 (p0) cc_final: 0.5516 (p0)
REVERT: B  110 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7270 (mtm180)
REVERT: B  255 PHE cc_start: 0.6177 (OUTLIER) cc_final: 0.5610 (m-80)
REVERT: B  304 LYS cc_start: 0.7663 (mtmm) cc_final: 0.7253 (mtmt)
REVERT: C   48 TYR cc_start: 0.0732 (OUTLIER) cc_final: -0.1914 (m-80)
REVERT: C  110 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7422 (mtm180)
REVERT: C  225 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7093 (tt0)
REVERT: C  255 PHE cc_start: 0.5830 (OUTLIER) cc_final: 0.5052 (m-80)
REVERT: D   48 TYR cc_start: 0.0682 (OUTLIER) cc_final: -0.0796 (m-10)
REVERT: D  102 ASN cc_start: 0.5710 (p0) cc_final: 0.5484 (p0)
REVERT: D  110 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7205 (mtm180)
REVERT: D  155 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8471 (m)
REVERT: D  255 PHE cc_start: 0.6022 (OUTLIER) cc_final: 0.5668 (m-80)
REVERT: E   48 TYR cc_start: 0.0411 (OUTLIER) cc_final: -0.1118 (m-10)
REVERT: E  102 ASN cc_start: 0.5836 (p0) cc_final: 0.5541 (p0)
REVERT: E  110 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7300 (mtt180)
REVERT: E  255 PHE cc_start: 0.6078 (OUTLIER) cc_final: 0.5260 (m-80)
REVERT: E  300 ASN cc_start: 0.5632 (p0) cc_final: 0.5376 (p0)
  outliers start: 94
  outliers final: 68
  residues processed: 214
  average time/residue: 0.2446
  time to fit residues: 77.4755
Evaluate side-chains
  218 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 132
  time to evaluate  : 1.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   68 ASP
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  161 ASN
Chi-restraints excluded: chain A residue  181 TRP
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue   48 TYR
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  110 ARG
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain B residue  181 TRP
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain B residue  432 PHE
Chi-restraints excluded: chain C residue   48 TYR
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue   68 ASP
Chi-restraints excluded: chain C residue  104 SER
Chi-restraints excluded: chain C residue  110 ARG
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  211 THR
Chi-restraints excluded: chain C residue  225 GLU
Chi-restraints excluded: chain C residue  255 PHE
Chi-restraints excluded: chain C residue  316 PHE
Chi-restraints excluded: chain C residue  432 PHE
Chi-restraints excluded: chain D residue   48 TYR
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain D residue  110 ARG
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  155 THR
Chi-restraints excluded: chain D residue  161 ASN
Chi-restraints excluded: chain D residue  181 TRP
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  211 THR
Chi-restraints excluded: chain D residue  218 LEU
Chi-restraints excluded: chain D residue  220 THR
Chi-restraints excluded: chain D residue  230 THR
Chi-restraints excluded: chain D residue  234 LEU
Chi-restraints excluded: chain D residue  255 PHE
Chi-restraints excluded: chain D residue  312 ILE
Chi-restraints excluded: chain D residue  316 PHE
Chi-restraints excluded: chain E residue   48 TYR
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue  104 SER
Chi-restraints excluded: chain E residue  110 ARG
Chi-restraints excluded: chain E residue  128 SER
Chi-restraints excluded: chain E residue  140 ILE
Chi-restraints excluded: chain E residue  161 ASN
Chi-restraints excluded: chain E residue  181 TRP
Chi-restraints excluded: chain E residue  205 LEU
Chi-restraints excluded: chain E residue  211 THR
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  220 THR
Chi-restraints excluded: chain E residue  255 PHE
Chi-restraints excluded: chain E residue  312 ILE
Chi-restraints excluded: chain E residue  316 PHE
Chi-restraints excluded: chain E residue  432 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 143 optimal weight:    0.7980
   chunk 130 optimal weight:    6.9990
   chunk 139 optimal weight:    1.9990
   chunk 83 optimal weight:   10.0000
   chunk 60 optimal weight:   20.0000
   chunk 109 optimal weight:    1.9990
   chunk 42 optimal weight:    0.3980
   chunk 125 optimal weight:    0.0770
   chunk 131 optimal weight:    0.5980
   chunk 138 optimal weight:    0.8980
   chunk 91 optimal weight:   20.0000
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
A 102 ASN
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 204 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.2934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13545  Z= 0.181
  Angle     :  0.661  11.360  18435  Z= 0.317
  Chirality :  0.045   0.234   2185
  Planarity :  0.003   0.032   2235
  Dihedral  :  8.008  45.890   2270
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  3.27 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 33.08 %
    Favored  : 62.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.22), residues: 1560
  helix:  2.48 (0.24), residues: 500
  sheet: -0.60 (0.25), residues: 335
  loop : -1.55 (0.23), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP D 261 
 HIS   0.005   0.001   HIS E 204 
 PHE   0.031   0.001   PHE B  99 
 TYR   0.017   0.001   TYR D 121 
 ARG   0.005   0.000   ARG C  91 

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 143
  time to evaluate  : 1.498 
Fit side-chains
REVERT: A   48 TYR cc_start: 0.0427 (OUTLIER) cc_final: -0.1659 (m-80)
REVERT: A  102 ASN cc_start: 0.5984 (p0) cc_final: 0.5703 (p0)
REVERT: A  155 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8416 (m)
REVERT: A  318 PHE cc_start: 0.6712 (OUTLIER) cc_final: 0.6305 (p90)
REVERT: B   48 TYR cc_start: 0.0507 (OUTLIER) cc_final: -0.1371 (m-80)
REVERT: B  102 ASN cc_start: 0.5783 (p0) cc_final: 0.5535 (p0)
REVERT: B  110 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7177 (mtm180)
REVERT: C   48 TYR cc_start: 0.0728 (OUTLIER) cc_final: -0.1963 (m-80)
REVERT: C  255 PHE cc_start: 0.5768 (OUTLIER) cc_final: 0.4963 (m-80)
REVERT: D   48 TYR cc_start: 0.0664 (OUTLIER) cc_final: -0.0775 (m-10)
REVERT: D  102 ASN cc_start: 0.5658 (p0) cc_final: 0.5434 (p0)
REVERT: D  155 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8426 (m)
REVERT: D  255 PHE cc_start: 0.6076 (OUTLIER) cc_final: 0.5730 (m-80)
REVERT: D  322 LEU cc_start: 0.6112 (OUTLIER) cc_final: 0.5882 (pt)
REVERT: E   48 TYR cc_start: 0.0406 (OUTLIER) cc_final: -0.1375 (m-80)
REVERT: E  102 ASN cc_start: 0.5837 (p0) cc_final: 0.5533 (p0)
REVERT: E  255 PHE cc_start: 0.6018 (OUTLIER) cc_final: 0.5229 (m-80)
  outliers start: 57
  outliers final: 38
  residues processed: 189
  average time/residue: 0.2247
  time to fit residues: 64.7171
Evaluate side-chains
  191 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 140
  time to evaluate  : 1.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  181 TRP
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue   48 TYR
Chi-restraints excluded: chain B residue   53 ARG
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  110 ARG
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  181 TRP
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain C residue   48 TYR
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue   68 ASP
Chi-restraints excluded: chain C residue  104 SER
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  211 THR
Chi-restraints excluded: chain C residue  255 PHE
Chi-restraints excluded: chain C residue  316 PHE
Chi-restraints excluded: chain D residue   48 TYR
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  155 THR
Chi-restraints excluded: chain D residue  181 TRP
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  255 PHE
Chi-restraints excluded: chain D residue  322 LEU
Chi-restraints excluded: chain E residue   48 TYR
Chi-restraints excluded: chain E residue  128 SER
Chi-restraints excluded: chain E residue  140 ILE
Chi-restraints excluded: chain E residue  181 TRP
Chi-restraints excluded: chain E residue  205 LEU
Chi-restraints excluded: chain E residue  255 PHE
Chi-restraints excluded: chain E residue  316 PHE
Chi-restraints excluded: chain E residue  432 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 147 optimal weight:    9.9990
   chunk 89 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 102 optimal weight:    4.9990
   chunk 154 optimal weight:    8.9990
   chunk 142 optimal weight:    2.9990
   chunk 122 optimal weight:   20.0000
   chunk 12 optimal weight:    5.9990
   chunk 94 optimal weight:    0.8980
   chunk 75 optimal weight:    0.8980
   chunk 97 optimal weight:    2.9990
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN
E 204 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.3085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  13545  Z= 0.293
  Angle     :  0.704  11.025  18435  Z= 0.339
  Chirality :  0.047   0.237   2185
  Planarity :  0.004   0.029   2235
  Dihedral  :  7.986  45.699   2270
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  3.97 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 33.15 %
    Favored  : 63.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.22), residues: 1560
  helix:  2.48 (0.24), residues: 500
  sheet: -0.72 (0.24), residues: 335
  loop : -1.64 (0.23), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 261 
 HIS   0.005   0.001   HIS E 204 
 PHE   0.031   0.002   PHE B  99 
 TYR   0.013   0.001   TYR B 121 
 ARG   0.004   0.000   ARG C  91 

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 141
  time to evaluate  : 1.361 
Fit side-chains
REVERT: A   48 TYR cc_start: 0.0485 (OUTLIER) cc_final: -0.1554 (m-80)
REVERT: A  102 ASN cc_start: 0.6000 (p0) cc_final: 0.5738 (p0)
REVERT: A  155 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8434 (m)
REVERT: A  234 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8305 (tp)
REVERT: A  318 PHE cc_start: 0.6770 (OUTLIER) cc_final: 0.6393 (p90)
REVERT: B   48 TYR cc_start: 0.0449 (OUTLIER) cc_final: -0.1369 (m-80)
REVERT: B  102 ASN cc_start: 0.5853 (p0) cc_final: 0.5601 (p0)
REVERT: B  110 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7208 (mtm180)
REVERT: B  255 PHE cc_start: 0.6184 (OUTLIER) cc_final: 0.5713 (m-80)
REVERT: C   48 TYR cc_start: 0.0735 (OUTLIER) cc_final: -0.1976 (m-80)
REVERT: C  110 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7357 (mtm180)
REVERT: C  255 PHE cc_start: 0.5901 (OUTLIER) cc_final: 0.5045 (m-80)
REVERT: D   48 TYR cc_start: 0.0616 (OUTLIER) cc_final: -0.1146 (m-80)
REVERT: D  155 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8442 (m)
REVERT: D  322 LEU cc_start: 0.6095 (OUTLIER) cc_final: 0.5848 (pt)
REVERT: E   48 TYR cc_start: 0.0415 (OUTLIER) cc_final: -0.1388 (m-80)
REVERT: E  110 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7267 (mtt180)
REVERT: E  255 PHE cc_start: 0.6073 (OUTLIER) cc_final: 0.5315 (m-80)
  outliers start: 55
  outliers final: 37
  residues processed: 184
  average time/residue: 0.2379
  time to fit residues: 65.7521
Evaluate side-chains
  186 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 133
  time to evaluate  : 1.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  181 TRP
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue   48 TYR
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  110 ARG
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  181 TRP
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain C residue   48 TYR
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue   68 ASP
Chi-restraints excluded: chain C residue  104 SER
Chi-restraints excluded: chain C residue  110 ARG
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  211 THR
Chi-restraints excluded: chain C residue  255 PHE
Chi-restraints excluded: chain C residue  316 PHE
Chi-restraints excluded: chain D residue   48 TYR
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  155 THR
Chi-restraints excluded: chain D residue  181 TRP
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  316 PHE
Chi-restraints excluded: chain D residue  322 LEU
Chi-restraints excluded: chain E residue   48 TYR
Chi-restraints excluded: chain E residue  110 ARG
Chi-restraints excluded: chain E residue  128 SER
Chi-restraints excluded: chain E residue  140 ILE
Chi-restraints excluded: chain E residue  181 TRP
Chi-restraints excluded: chain E residue  205 LEU
Chi-restraints excluded: chain E residue  255 PHE
Chi-restraints excluded: chain E residue  316 PHE
Chi-restraints excluded: chain E residue  432 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 130 optimal weight:    0.9980
   chunk 37 optimal weight:    6.9990
   chunk 113 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 123 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 126 optimal weight:    0.2980
   chunk 15 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 108 optimal weight:    2.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 204 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.238874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.205390 restraints weight = 13198.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.4203 rms_B_bonded: 1.15
r_work: 0.3877 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3554 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.3175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13545  Z= 0.270
  Angle     :  0.694  11.186  18435  Z= 0.334
  Chirality :  0.047   0.241   2185
  Planarity :  0.003   0.030   2235
  Dihedral  :  7.772  45.922   2270
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  3.78 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 33.15 %
    Favored  : 62.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.22), residues: 1560
  helix:  2.48 (0.24), residues: 500
  sheet: -0.73 (0.24), residues: 335
  loop : -1.62 (0.23), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 261 
 HIS   0.005   0.001   HIS E 204 
 PHE   0.030   0.002   PHE B  99 
 TYR   0.012   0.001   TYR C 433 
 ARG   0.004   0.000   ARG E  91 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2563.47 seconds
wall clock time: 48 minutes 17.70 seconds (2897.70 seconds total)