Starting phenix.real_space_refine
on Sat Aug 23 15:50:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vsz_43512/08_2025/8vsz_43512.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vsz_43512/08_2025/8vsz_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_43512/08_2025/8vsz_43512.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vsz_43512/08_2025/8vsz_43512.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vsz_43512/08_2025/8vsz_43512.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vsz_43512/08_2025/8vsz_43512.cif"
  }
  resolution = 3.07
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: "F"
      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:
    B, C, D, E, G, H, I, J
  Time building chain proxies: 2.77, per 1000 atoms: 0.21
  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=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 160 " - pdb=" SG  CYS A 174 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 160 " - pdb=" SG  CYS B 174 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 160 " - pdb=" SG  CYS C 174 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 160 " - pdb=" SG  CYS D 174 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 160 " - pdb=" SG  CYS E 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: 1.69
  Conformation dependent library (CDL) restraints added in 603.6 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  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: 0.53
  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: 2.46

  Time building geometry restraints manager: 2.15 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: 919
       43.80 -    65.69: 117
       65.69 -    87.59: 45
       87.59 -   109.49: 25
  Dihedral angle restraints: 8190
    sinusoidal: 3510
      harmonic: 4680
  Sorted by residual:
  dihedral pdb=" CB  CYS C 160 "
           pdb=" SG  CYS C 160 "
           pdb=" SG  CYS C 174 "
           pdb=" CB  CYS C 174 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   49.47   43.53     1      1.00e+01 1.00e-02 2.64e+01
  dihedral pdb=" CB  CYS B 160 "
           pdb=" SG  CYS B 160 "
           pdb=" SG  CYS B 174 "
           pdb=" CB  CYS B 174 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   49.47   43.53     1      1.00e+01 1.00e-02 2.64e+01
  dihedral pdb=" CB  CYS E 160 "
           pdb=" SG  CYS E 160 "
           pdb=" SG  CYS E 174 "
           pdb=" CB  CYS E 174 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   49.47   43.53     1      1.00e+01 1.00e-02 2.64e+01
  ... (remaining 8187 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:
        2.23 -     2.77: 2285
        2.77 -     3.30: 12369
        3.30 -     3.83: 22277
        3.83 -     4.37: 25923
        4.37 -     4.90: 44665
  Nonbonded interactions: 107519
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 180 "
            pdb=" O   TYR B 183 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OG  SER D 180 "
            pdb=" O   TYR D 183 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OG  SER C 180 "
            pdb=" O   TYR C 183 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OG  SER E 180 "
            pdb=" O   TYR E 183 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OG  SER A 180 "
            pdb=" O   TYR A 183 "
     model   vdw
     2.234 3.040
  ... (remaining 107514 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: 0.03
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:             2.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     14.020
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.110
-------------------------------------------------------------------------------
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  13580  Z= 0.157
  Angle     :  0.664   7.879  18520  Z= 0.324
  Chirality :  0.047   0.296   2185
  Planarity :  0.002   0.023   2235
  Dihedral  : 19.650 109.487   5165
  Min Nonbonded Distance : 2.233

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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG C  53 
 TYR   0.011   0.001   TYR D 433 
 PHE   0.014   0.001   PHE E 318 
 TRP   0.017   0.002   TRP B 261 
 HIS   0.004   0.001   HIS C 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (13545)
  covalent geometry    : angle       0.64952 (18435)
  SS BOND              : bond        0.00162 (    5)
  SS BOND              : angle       0.33597 (   10)
  hydrogen bonds       : bond        0.18703 (  625)
  hydrogen bonds       : angle       7.70836 ( 2220)
  Misc. bond           : bond        0.00025 (    5)
  link_ALPHA1-4        : bond        0.00675 (    5)
  link_ALPHA1-4        : angle       1.46442 (   15)
  link_BETA1-4         : bond        0.00472 (   10)
  link_BETA1-4         : angle       1.30839 (   30)
  link_NAG-ASN         : bond        0.00689 (   10)
  link_NAG-ASN         : angle       3.23518 (   30)

*********************** 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  : 0.476 
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: 0.1102
  time to fit residues: 21.3299
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  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    9.9990
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:   10.0000
   chunk 149 optimal weight:    7.9990
   overall best weight:    2.3786

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.235871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.200632 restraints weight = 13267.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.4168 rms_B_bonded: 1.32
r_work: 0.3769 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3486 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.1516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.073  13580  Z= 0.256
  Angle     :  0.742   6.850  18520  Z= 0.365
  Chirality :  0.050   0.346   2185
  Planarity :  0.004   0.029   2235
  Dihedral  : 11.733  80.444   2270
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  3.85 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 31.54 %
    Favored  : 64.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.40 (0.22), residues: 1560
  helix:  2.47 (0.24), residues: 495
  sheet: -1.04 (0.26), residues: 315
  loop : -1.88 (0.22), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 153 
 TYR   0.014   0.002   TYR E 121 
 PHE   0.021   0.002   PHE D 316 
 TRP   0.017   0.003   TRP B 261 
 HIS   0.005   0.002   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00599 (13545)
  covalent geometry    : angle       0.72088 (18435)
  SS BOND              : bond        0.00704 (    5)
  SS BOND              : angle       1.81314 (   10)
  hydrogen bonds       : bond        0.04860 (  625)
  hydrogen bonds       : angle       4.94737 ( 2220)
  Misc. bond           : bond        0.00081 (    5)
  link_ALPHA1-4        : bond        0.00944 (    5)
  link_ALPHA1-4        : angle       3.27559 (   15)
  link_BETA1-4         : bond        0.00594 (   10)
  link_BETA1-4         : angle       2.34739 (   30)
  link_NAG-ASN         : bond        0.00265 (   10)
  link_NAG-ASN         : angle       2.94337 (   30)

*********************** 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
  210 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 148
  time to evaluate  : 0.423 
Fit side-chains
REVERT: A   93 MET cc_start: 0.7755 (tpp) cc_final: 0.7547 (tpp)
REVERT: A  234 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8107 (tp)
REVERT: A  318 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.6969 (p90)
REVERT: B   48 TYR cc_start: -0.0506 (OUTLIER) cc_final: -0.1616 (m-10)
REVERT: C  295 SER cc_start: 0.6132 (OUTLIER) cc_final: 0.5123 (t)
REVERT: C  304 LYS cc_start: 0.7615 (mtmm) cc_final: 0.7071 (mtmt)
REVERT: D  318 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.7126 (p90)
REVERT: E   48 TYR cc_start: 0.0136 (OUTLIER) cc_final: -0.2811 (m-80)
REVERT: E  304 LYS cc_start: 0.7746 (mtmm) cc_final: 0.7226 (mtmt)
  outliers start: 62
  outliers final: 34
  residues processed: 200
  average time/residue: 0.1011
  time to fit residues: 31.4272
Evaluate side-chains
  167 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 127
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
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  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  128 SER
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  104 SER
Chi-restraints excluded: chain C residue  128 SER
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   61 VAL
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain D residue  128 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   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  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 109 optimal weight:    7.9990
   chunk 28 optimal weight:   30.0000
   chunk 143 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 94 optimal weight:    0.0980
   chunk 106 optimal weight:    1.9990
   chunk 61 optimal weight:   10.0000
   chunk 31 optimal weight:    4.9990
   chunk 24 optimal weight:    8.9990
   chunk 142 optimal weight:    0.8980
   chunk 119 optimal weight:    1.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4514 r_free = 0.4514 target = 0.238389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.206993 restraints weight = 13406.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.4228 rms_B_bonded: 1.23
r_work: 0.3846 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3538 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.1626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13580  Z= 0.145
  Angle     :  0.649  11.058  18520  Z= 0.311
  Chirality :  0.045   0.297   2185
  Planarity :  0.003   0.025   2235
  Dihedral  : 10.808  71.307   2270
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  2.69 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 32.52 %
    Favored  : 62.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.22 (0.22), residues: 1560
  helix:  2.51 (0.24), residues: 495
  sheet: -0.84 (0.26), residues: 315
  loop : -1.75 (0.23), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 221 
 TYR   0.013   0.001   TYR D 121 
 PHE   0.019   0.001   PHE D 316 
 TRP   0.018   0.002   TRP A 261 
 HIS   0.006   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (13545)
  covalent geometry    : angle       0.62830 (18435)
  SS BOND              : bond        0.00588 (    5)
  SS BOND              : angle       1.39830 (   10)
  hydrogen bonds       : bond        0.04297 (  625)
  hydrogen bonds       : angle       4.42586 ( 2220)
  Misc. bond           : bond        0.00059 (    5)
  link_ALPHA1-4        : bond        0.01147 (    5)
  link_ALPHA1-4        : angle       2.28232 (   15)
  link_BETA1-4         : bond        0.00604 (   10)
  link_BETA1-4         : angle       2.64346 (   30)
  link_NAG-ASN         : bond        0.00491 (   10)
  link_NAG-ASN         : angle       2.63835 (   30)

*********************** 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
  204 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 138
  time to evaluate  : 0.522 
Fit side-chains
REVERT: A  234 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8078 (tp)
REVERT: A  247 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7036 (tt)
REVERT: A  295 SER cc_start: 0.5677 (OUTLIER) cc_final: 0.4979 (t)
REVERT: A  318 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.6973 (p90)
REVERT: B  110 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.7093 (mtm180)
REVERT: C   48 TYR cc_start: -0.0141 (OUTLIER) cc_final: -0.2511 (m-80)
REVERT: C  110 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7139 (mtm180)
REVERT: C  304 LYS cc_start: 0.7577 (mtmm) cc_final: 0.7056 (mtmt)
REVERT: D   48 TYR cc_start: -0.0160 (OUTLIER) cc_final: -0.1160 (m-10)
REVERT: D  110 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.7144 (mtm180)
REVERT: D  295 SER cc_start: 0.6100 (OUTLIER) cc_final: 0.5271 (t)
REVERT: D  318 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.7164 (p90)
REVERT: E  110 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.7139 (mtt180)
REVERT: E  295 SER cc_start: 0.6210 (OUTLIER) cc_final: 0.5432 (t)
REVERT: E  304 LYS cc_start: 0.7701 (mtmm) cc_final: 0.7176 (mtmt)
  outliers start: 66
  outliers final: 33
  residues processed: 191
  average time/residue: 0.1503
  time to fit residues: 39.6980
Evaluate side-chains
  179 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 133
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
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  247 LEU
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  110 ARG
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  211 THR
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  242 VAL
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  110 ARG
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  242 VAL
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   61 VAL
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain D residue  110 ARG
Chi-restraints excluded: chain D residue  181 TRP
Chi-restraints excluded: chain D residue  234 LEU
Chi-restraints excluded: chain D residue  295 SER
Chi-restraints excluded: chain D residue  318 PHE
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  181 TRP
Chi-restraints excluded: chain E residue  211 THR
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 16 optimal weight:    0.0980
   chunk 11 optimal weight:    1.9990
   chunk 70 optimal weight:    0.4980
   chunk 36 optimal weight:   10.0000
   chunk 106 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 108 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   chunk 79 optimal weight:    3.9990
   chunk 83 optimal weight:   10.0000
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.242001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.208290 restraints weight = 13258.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.4222 rms_B_bonded: 1.21
r_work: 0.3865 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3607 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  13580  Z= 0.124
  Angle     :  0.632  11.185  18520  Z= 0.301
  Chirality :  0.044   0.253   2185
  Planarity :  0.003   0.025   2235
  Dihedral  :  9.814  63.735   2270
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  3.14 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 31.54 %
    Favored  : 63.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.04 (0.22), residues: 1560
  helix:  2.60 (0.23), residues: 495
  sheet: -0.79 (0.25), residues: 340
  loop : -1.45 (0.23), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  91 
 TYR   0.012   0.001   TYR C 433 
 PHE   0.020   0.001   PHE D 316 
 TRP   0.018   0.002   TRP A 261 
 HIS   0.003   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (13545)
  covalent geometry    : angle       0.61404 (18435)
  SS BOND              : bond        0.00451 (    5)
  SS BOND              : angle       1.10069 (   10)
  hydrogen bonds       : bond        0.03858 (  625)
  hydrogen bonds       : angle       4.03914 ( 2220)
  Misc. bond           : bond        0.00051 (    5)
  link_ALPHA1-4        : bond        0.01232 (    5)
  link_ALPHA1-4        : angle       2.36275 (   15)
  link_BETA1-4         : bond        0.00655 (   10)
  link_BETA1-4         : angle       2.84921 (   30)
  link_NAG-ASN         : bond        0.00436 (   10)
  link_NAG-ASN         : angle       1.96558 (   30)

*********************** 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
  210 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 137
  time to evaluate  : 0.475 
Fit side-chains
REVERT: A   48 TYR cc_start: -0.0290 (OUTLIER) cc_final: -0.2352 (m-80)
REVERT: A  155 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8173 (m)
REVERT: A  234 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8065 (tp)
REVERT: A  247 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7094 (tt)
REVERT: A  318 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.7001 (p90)
REVERT: B   48 TYR cc_start: -0.0370 (OUTLIER) cc_final: -0.1605 (m-10)
REVERT: B  110 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.7042 (mtm180)
REVERT: B  255 PHE cc_start: 0.5535 (OUTLIER) cc_final: 0.4722 (m-80)
REVERT: B  304 LYS cc_start: 0.7265 (mtmt) cc_final: 0.6947 (mtmm)
REVERT: C   48 TYR cc_start: -0.0093 (OUTLIER) cc_final: -0.2462 (m-80)
REVERT: C  110 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.7024 (mtm180)
REVERT: C  304 LYS cc_start: 0.7612 (mtmm) cc_final: 0.7084 (mtmt)
REVERT: D   48 TYR cc_start: -0.0077 (OUTLIER) cc_final: -0.1197 (m-10)
REVERT: D  110 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.7018 (mtm180)
REVERT: D  318 PHE cc_start: 0.7538 (OUTLIER) cc_final: 0.7128 (p90)
REVERT: E   48 TYR cc_start: 0.0208 (OUTLIER) cc_final: -0.2659 (m-80)
REVERT: E  110 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.7066 (mtt180)
REVERT: E  285 MET cc_start: 0.7853 (tpt) cc_final: 0.7563 (tpt)
REVERT: E  304 LYS cc_start: 0.7658 (mtmm) cc_final: 0.7209 (mtmt)
  outliers start: 73
  outliers final: 27
  residues processed: 198
  average time/residue: 0.1200
  time to fit residues: 34.9390
Evaluate side-chains
  179 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 137
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
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  155 THR
Chi-restraints excluded: chain A residue  181 TRP
Chi-restraints excluded: chain A residue  215 TYR
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  247 LEU
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  133 VAL
Chi-restraints excluded: chain B residue  181 TRP
Chi-restraints excluded: chain B residue  191 THR
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  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  133 VAL
Chi-restraints excluded: chain C residue  181 TRP
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   61 VAL
Chi-restraints excluded: chain D residue  110 ARG
Chi-restraints excluded: chain D residue  181 TRP
Chi-restraints excluded: chain D residue  191 THR
Chi-restraints excluded: chain D residue  211 THR
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain E residue   48 TYR
Chi-restraints excluded: chain E residue  104 SER
Chi-restraints excluded: chain E residue  110 ARG
Chi-restraints excluded: chain E residue  181 TRP
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  242 VAL
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 76 optimal weight:    4.9990
   chunk 105 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   chunk 126 optimal weight:    2.9990
   chunk 130 optimal weight:    5.9990
   chunk 100 optimal weight:    2.9990
   chunk 123 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 57 optimal weight:    9.9990
   chunk 106 optimal weight:    0.7980
   overall best weight:    2.1586

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4879 r_free = 0.4879 target = 0.267439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4698 r_free = 0.4698 target = 0.246955 restraints weight = 13612.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.4661 rms_B_bonded: 0.79
r_work: 0.4372 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work (final): 0.4372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7170
moved from start:          0.2340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  13580  Z= 0.236
  Angle     :  0.738  10.934  18520  Z= 0.353
  Chirality :  0.048   0.270   2185
  Planarity :  0.004   0.029   2235
  Dihedral  :  9.583  57.804   2270
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  3.97 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  6.36 %
    Allowed  : 30.84 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.22), residues: 1560
  helix:  2.55 (0.24), residues: 500
  sheet: -0.94 (0.25), residues: 340
  loop : -1.65 (0.23), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  91 
 TYR   0.014   0.002   TYR B 309 
 PHE   0.018   0.002   PHE E 316 
 TRP   0.017   0.002   TRP B 261 
 HIS   0.013   0.002   HIS C 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00543 (13545)
  covalent geometry    : angle       0.71934 (18435)
  SS BOND              : bond        0.00740 (    5)
  SS BOND              : angle       1.77351 (   10)
  hydrogen bonds       : bond        0.04034 (  625)
  hydrogen bonds       : angle       4.35752 ( 2220)
  Misc. bond           : bond        0.00076 (    5)
  link_ALPHA1-4        : bond        0.00827 (    5)
  link_ALPHA1-4        : angle       3.39642 (   15)
  link_BETA1-4         : bond        0.00535 (   10)
  link_BETA1-4         : angle       2.67193 (   30)
  link_NAG-ASN         : bond        0.00155 (   10)
  link_NAG-ASN         : angle       2.02252 (   30)

*********************** 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
  234 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 91
    poor density    : 143
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A   48 TYR cc_start: 0.0990 (OUTLIER) cc_final: -0.1423 (m-80)
REVERT: A  234 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7869 (tp)
REVERT: A  318 PHE cc_start: 0.6424 (OUTLIER) cc_final: 0.5886 (p90)
REVERT: B   48 TYR cc_start: 0.1128 (OUTLIER) cc_final: -0.0492 (m-10)
REVERT: B  110 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.7058 (mtm180)
REVERT: B  255 PHE cc_start: 0.5487 (OUTLIER) cc_final: 0.4848 (m-80)
REVERT: C   48 TYR cc_start: 0.1489 (OUTLIER) cc_final: -0.1721 (m-80)
REVERT: C  110 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7181 (mtm180)
REVERT: C  255 PHE cc_start: 0.5328 (OUTLIER) cc_final: 0.4807 (m-80)
REVERT: C  304 LYS cc_start: 0.7674 (mtmm) cc_final: 0.7411 (mtmt)
REVERT: D   48 TYR cc_start: 0.1109 (OUTLIER) cc_final: -0.0378 (m-10)
REVERT: D  110 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7088 (mtm180)
REVERT: D  318 PHE cc_start: 0.6083 (OUTLIER) cc_final: 0.5781 (p90)
REVERT: E   48 TYR cc_start: 0.1122 (OUTLIER) cc_final: -0.1990 (m-80)
REVERT: E  110 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7215 (mtt180)
REVERT: E  255 PHE cc_start: 0.5395 (OUTLIER) cc_final: 0.4893 (m-80)
  outliers start: 91
  outliers final: 54
  residues processed: 218
  average time/residue: 0.0999
  time to fit residues: 32.5844
Evaluate side-chains
  200 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 131
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
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  104 SER
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  161 ASN
Chi-restraints excluded: chain A residue  181 TRP
Chi-restraints excluded: chain A residue  188 VAL
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  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  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  242 VAL
Chi-restraints excluded: chain B residue  255 PHE
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  242 VAL
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   61 VAL
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  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  234 LEU
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  133 VAL
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  255 PHE
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 45 optimal weight:    3.9990
   chunk 131 optimal weight:    1.9990
   chunk 112 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 71 optimal weight:    0.2980
   chunk 106 optimal weight:    0.6980
   chunk 118 optimal weight:    0.0010
   chunk 51 optimal weight:    0.9990
   chunk 5 optimal weight:    9.9990
   chunk 23 optimal weight:    7.9990
   chunk 47 optimal weight:    0.0170
   overall best weight:    0.4026

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.240255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.200449 restraints weight = 13308.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.4174 rms_B_bonded: 1.35
r_work: 0.3779 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  13580  Z= 0.122
  Angle     :  0.645  11.240  18520  Z= 0.305
  Chirality :  0.044   0.229   2185
  Planarity :  0.003   0.027   2235
  Dihedral  :  8.974  55.196   2270
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  2.82 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 32.52 %
    Favored  : 63.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.22), residues: 1560
  helix:  2.61 (0.24), residues: 500
  sheet: -0.70 (0.25), residues: 340
  loop : -1.44 (0.24), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  91 
 TYR   0.015   0.001   TYR C 433 
 PHE   0.017   0.001   PHE B 316 
 TRP   0.019   0.001   TRP E 261 
 HIS   0.002   0.001   HIS C 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (13545)
  covalent geometry    : angle       0.62719 (18435)
  SS BOND              : bond        0.00443 (    5)
  SS BOND              : angle       1.03015 (   10)
  hydrogen bonds       : bond        0.03741 (  625)
  hydrogen bonds       : angle       3.87894 ( 2220)
  Misc. bond           : bond        0.00051 (    5)
  link_ALPHA1-4        : bond        0.01271 (    5)
  link_ALPHA1-4        : angle       2.20336 (   15)
  link_BETA1-4         : bond        0.00649 (   10)
  link_BETA1-4         : angle       2.91610 (   30)
  link_NAG-ASN         : bond        0.00372 (   10)
  link_NAG-ASN         : angle       1.87683 (   30)

*********************** 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
  205 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 146
  time to evaluate  : 0.580 
Fit side-chains
REVERT: A   48 TYR cc_start: 0.0345 (OUTLIER) cc_final: -0.1917 (m-80)
REVERT: A  155 THR cc_start: 0.8310 (OUTLIER) cc_final: 0.8087 (m)
REVERT: A  204 HIS cc_start: 0.5690 (m90) cc_final: 0.5471 (m-70)
REVERT: A  318 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6623 (p90)
REVERT: B   48 TYR cc_start: 0.0400 (OUTLIER) cc_final: -0.1037 (m-10)
REVERT: B  102 ASN cc_start: 0.5748 (p0) cc_final: 0.5392 (p0)
REVERT: B  110 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7048 (mtm180)
REVERT: B  304 LYS cc_start: 0.7673 (mtmm) cc_final: 0.7258 (mtmt)
REVERT: C   48 TYR cc_start: 0.0731 (OUTLIER) cc_final: -0.2031 (m-80)
REVERT: C  108 ASP cc_start: 0.7776 (m-30) cc_final: 0.7535 (m-30)
REVERT: C  110 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.7080 (mtm180)
REVERT: C  255 PHE cc_start: 0.5651 (OUTLIER) cc_final: 0.4720 (m-80)
REVERT: C  304 LYS cc_start: 0.7724 (mtmm) cc_final: 0.7212 (mtmt)
REVERT: D   48 TYR cc_start: 0.0566 (OUTLIER) cc_final: -0.0746 (m-10)
REVERT: D  110 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7215 (mtm180)
REVERT: D  318 PHE cc_start: 0.7009 (OUTLIER) cc_final: 0.6722 (p90)
REVERT: E   48 TYR cc_start: 0.0814 (OUTLIER) cc_final: -0.2195 (m-80)
REVERT: E  110 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7128 (mtt180)
REVERT: E  285 MET cc_start: 0.8024 (tpt) cc_final: 0.7727 (tpt)
  outliers start: 59
  outliers final: 36
  residues processed: 190
  average time/residue: 0.1117
  time to fit residues: 31.6708
Evaluate side-chains
  184 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 135
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
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  142 LEU
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  181 TRP
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  110 ARG
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  242 VAL
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  215 TYR
Chi-restraints excluded: chain C residue  234 LEU
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   61 VAL
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  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  316 PHE
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain E residue   48 TYR
Chi-restraints excluded: chain E residue  104 SER
Chi-restraints excluded: chain E residue  110 ARG
Chi-restraints excluded: chain E residue  181 TRP
Chi-restraints excluded: chain E residue  205 LEU
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 2 optimal weight:    3.9990
   chunk 106 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 20 optimal weight:   10.0000
   chunk 83 optimal weight:    0.9980
   chunk 112 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0370
   chunk 64 optimal weight:    3.9990
   chunk 149 optimal weight:    9.9990
   chunk 4 optimal weight:    0.9990
   chunk 58 optimal weight:    8.9990
   overall best weight:    1.0062

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.238154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.196658 restraints weight = 13191.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.4148 rms_B_bonded: 1.45
r_work: 0.3736 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.2452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  13580  Z= 0.148
  Angle     :  0.660  11.129  18520  Z= 0.314
  Chirality :  0.045   0.229   2185
  Planarity :  0.003   0.027   2235
  Dihedral  :  8.640  52.729   2270
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  2.95 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 31.89 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.22), residues: 1560
  helix:  2.65 (0.24), residues: 500
  sheet: -0.66 (0.25), residues: 340
  loop : -1.46 (0.24), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  91 
 TYR   0.012   0.001   TYR C 433 
 PHE   0.032   0.002   PHE B  99 
 TRP   0.018   0.002   TRP B 261 
 HIS   0.003   0.001   HIS B 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (13545)
  covalent geometry    : angle       0.64193 (18435)
  SS BOND              : bond        0.00481 (    5)
  SS BOND              : angle       2.44806 (   10)
  hydrogen bonds       : bond        0.03693 (  625)
  hydrogen bonds       : angle       3.86538 ( 2220)
  Misc. bond           : bond        0.00063 (    5)
  link_ALPHA1-4        : bond        0.01083 (    5)
  link_ALPHA1-4        : angle       2.76868 (   15)
  link_BETA1-4         : bond        0.00603 (   10)
  link_BETA1-4         : angle       2.78559 (   30)
  link_NAG-ASN         : bond        0.00131 (   10)
  link_NAG-ASN         : angle       1.57590 (   30)

*********************** 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
  216 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 142
  time to evaluate  : 0.426 
Fit side-chains
REVERT: A   48 TYR cc_start: 0.0244 (OUTLIER) cc_final: -0.1980 (m-80)
REVERT: A  234 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7951 (tp)
REVERT: A  318 PHE cc_start: 0.7400 (OUTLIER) cc_final: 0.6681 (p90)
REVERT: B   48 TYR cc_start: 0.0405 (OUTLIER) cc_final: -0.1364 (m-80)
REVERT: B  102 ASN cc_start: 0.5861 (p0) cc_final: 0.5479 (p0)
REVERT: B  110 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.7069 (mtm180)
REVERT: B  304 LYS cc_start: 0.7743 (mtmm) cc_final: 0.7230 (mtmt)
REVERT: C   48 TYR cc_start: 0.0672 (OUTLIER) cc_final: -0.2101 (m-80)
REVERT: C  108 ASP cc_start: 0.7804 (m-30) cc_final: 0.7575 (m-30)
REVERT: C  110 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7103 (mtm180)
REVERT: C  304 LYS cc_start: 0.7709 (mtmm) cc_final: 0.7286 (mtmt)
REVERT: D   48 TYR cc_start: 0.0458 (OUTLIER) cc_final: -0.0900 (m-10)
REVERT: D  102 ASN cc_start: 0.5523 (p0) cc_final: 0.5298 (p0)
REVERT: D  110 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7239 (mtm180)
REVERT: D  255 PHE cc_start: 0.6101 (OUTLIER) cc_final: 0.5534 (m-80)
REVERT: D  318 PHE cc_start: 0.7095 (OUTLIER) cc_final: 0.6615 (p90)
REVERT: E   48 TYR cc_start: 0.0536 (OUTLIER) cc_final: -0.2359 (m-80)
REVERT: E  110 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7214 (mtt180)
REVERT: E  255 PHE cc_start: 0.5793 (OUTLIER) cc_final: 0.5061 (m-80)
REVERT: E  285 MET cc_start: 0.7989 (tpt) cc_final: 0.7708 (tpt)
  outliers start: 74
  outliers final: 46
  residues processed: 204
  average time/residue: 0.1076
  time to fit residues: 32.3406
Evaluate side-chains
  198 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 138
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
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  110 ARG
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  181 TRP
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  218 LEU
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  242 VAL
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  234 LEU
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   61 VAL
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  181 TRP
Chi-restraints excluded: chain D residue  205 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  181 TRP
Chi-restraints excluded: chain E residue  205 LEU
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  242 VAL
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 143 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 121 optimal weight:   40.0000
   chunk 39 optimal weight:    4.9990
   chunk 131 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 84 optimal weight:    8.9990
   chunk 114 optimal weight:    0.9990
   chunk 71 optimal weight:    0.0060
   chunk 10 optimal weight:    0.6980
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.8600

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.239082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.199275 restraints weight = 13140.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.4167 rms_B_bonded: 1.47
r_work: 0.3767 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13580  Z= 0.138
  Angle     :  0.659  11.330  18520  Z= 0.311
  Chirality :  0.045   0.223   2185
  Planarity :  0.003   0.030   2235
  Dihedral  :  8.313  50.481   2270
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  2.95 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 32.45 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.22), residues: 1560
  helix:  2.62 (0.24), residues: 500
  sheet: -0.64 (0.25), residues: 340
  loop : -1.43 (0.24), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  91 
 TYR   0.013   0.001   TYR C 433 
 PHE   0.027   0.002   PHE B  99 
 TRP   0.018   0.002   TRP B 261 
 HIS   0.005   0.001   HIS E 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (13545)
  covalent geometry    : angle       0.64199 (18435)
  SS BOND              : bond        0.00535 (    5)
  SS BOND              : angle       2.03892 (   10)
  hydrogen bonds       : bond        0.03624 (  625)
  hydrogen bonds       : angle       3.80958 ( 2220)
  Misc. bond           : bond        0.00060 (    5)
  link_ALPHA1-4        : bond        0.01158 (    5)
  link_ALPHA1-4        : angle       2.51851 (   15)
  link_BETA1-4         : bond        0.00634 (   10)
  link_BETA1-4         : angle       2.79776 (   30)
  link_NAG-ASN         : bond        0.00198 (   10)
  link_NAG-ASN         : angle       1.56971 (   30)

*********************** 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
  208 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 144
  time to evaluate  : 0.537 
Fit side-chains
REVERT: A   48 TYR cc_start: 0.0305 (OUTLIER) cc_final: -0.1854 (m-80)
REVERT: A  234 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7937 (tp)
REVERT: A  318 PHE cc_start: 0.7307 (OUTLIER) cc_final: 0.6712 (p90)
REVERT: B   48 TYR cc_start: 0.0465 (OUTLIER) cc_final: -0.1328 (m-80)
REVERT: B  102 ASN cc_start: 0.5828 (p0) cc_final: 0.5466 (p0)
REVERT: B  110 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.7018 (mtm180)
REVERT: B  304 LYS cc_start: 0.7687 (mtmm) cc_final: 0.7205 (mtmt)
REVERT: C   48 TYR cc_start: 0.0734 (OUTLIER) cc_final: -0.2071 (m-80)
REVERT: C  108 ASP cc_start: 0.7735 (m-30) cc_final: 0.7502 (m-30)
REVERT: C  110 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7119 (mtm180)
REVERT: C  172 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7465 (mt0)
REVERT: C  255 PHE cc_start: 0.5878 (OUTLIER) cc_final: 0.5125 (m-80)
REVERT: C  304 LYS cc_start: 0.7692 (mtmm) cc_final: 0.7308 (mtmt)
REVERT: D   48 TYR cc_start: 0.0533 (OUTLIER) cc_final: -0.1007 (m-10)
REVERT: D  102 ASN cc_start: 0.5525 (p0) cc_final: 0.5310 (p0)
REVERT: D  110 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7149 (mtm180)
REVERT: D  255 PHE cc_start: 0.6081 (OUTLIER) cc_final: 0.5552 (m-80)
REVERT: E   48 TYR cc_start: 0.0585 (OUTLIER) cc_final: -0.2337 (m-80)
REVERT: E  110 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7196 (mtt180)
REVERT: E  255 PHE cc_start: 0.5814 (OUTLIER) cc_final: 0.4792 (m-80)
REVERT: E  285 MET cc_start: 0.7981 (tpt) cc_final: 0.7721 (tpt)
  outliers start: 64
  outliers final: 43
  residues processed: 196
  average time/residue: 0.1214
  time to fit residues: 34.7938
Evaluate side-chains
  198 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 140
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
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  128 SER
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  181 TRP
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  242 VAL
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  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  234 LEU
Chi-restraints excluded: chain B residue  242 VAL
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  172 GLN
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  234 LEU
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   53 ARG
Chi-restraints excluded: chain D residue   61 VAL
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  181 TRP
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  234 LEU
Chi-restraints excluded: chain D residue  255 PHE
Chi-restraints excluded: chain D residue  316 PHE
Chi-restraints excluded: chain E residue   48 TYR
Chi-restraints excluded: chain E residue   53 ARG
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  218 LEU
Chi-restraints excluded: chain E residue  242 VAL
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 109 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   chunk 56 optimal weight:    9.9990
   chunk 16 optimal weight:    0.8980
   chunk 20 optimal weight:    0.3980
   chunk 24 optimal weight:    9.9990
   chunk 139 optimal weight:    0.9980
   chunk 112 optimal weight:    0.7980
   chunk 82 optimal weight:   10.0000
   chunk 13 optimal weight:    0.4980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 102 ASN
D 102 ASN
E 204 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.239759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.201918 restraints weight = 13259.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.4191 rms_B_bonded: 1.52
r_work: 0.3771 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.2654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13580  Z= 0.131
  Angle     :  0.650  11.113  18520  Z= 0.308
  Chirality :  0.044   0.216   2185
  Planarity :  0.003   0.028   2235
  Dihedral  :  7.900  47.241   2270
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  2.50 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 32.59 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.22), residues: 1560
  helix:  2.60 (0.24), residues: 500
  sheet: -0.66 (0.25), residues: 345
  loop : -1.38 (0.24), residues: 715

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  91 
 TYR   0.013   0.001   TYR C 433 
 PHE   0.026   0.001   PHE B  99 
 TRP   0.019   0.002   TRP D 261 
 HIS   0.004   0.001   HIS E 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (13545)
  covalent geometry    : angle       0.63400 (18435)
  SS BOND              : bond        0.00443 (    5)
  SS BOND              : angle       1.92343 (   10)
  hydrogen bonds       : bond        0.03538 (  625)
  hydrogen bonds       : angle       3.71989 ( 2220)
  Misc. bond           : bond        0.00058 (    5)
  link_ALPHA1-4        : bond        0.01163 (    5)
  link_ALPHA1-4        : angle       2.45823 (   15)
  link_BETA1-4         : bond        0.00626 (   10)
  link_BETA1-4         : angle       2.76739 (   30)
  link_NAG-ASN         : bond        0.00204 (   10)
  link_NAG-ASN         : angle       1.44676 (   30)

*********************** 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
  209 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 145
  time to evaluate  : 0.493 
Fit side-chains
REVERT: A   48 TYR cc_start: -0.0005 (OUTLIER) cc_final: -0.1918 (m-80)
REVERT: A  102 ASN cc_start: 0.6096 (p0) cc_final: 0.5678 (p0)
REVERT: A  318 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.6858 (p90)
REVERT: B   48 TYR cc_start: 0.0210 (OUTLIER) cc_final: -0.1562 (m-80)
REVERT: B  102 ASN cc_start: 0.5930 (p0) cc_final: 0.5541 (p0)
REVERT: B  110 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6932 (mtm180)
REVERT: C   48 TYR cc_start: 0.0440 (OUTLIER) cc_final: -0.2189 (m-80)
REVERT: C  102 ASN cc_start: 0.5934 (p0) cc_final: 0.5578 (p0)
REVERT: C  110 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7151 (mtm180)
REVERT: C  172 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7409 (mt0)
REVERT: C  255 PHE cc_start: 0.5815 (OUTLIER) cc_final: 0.5004 (m-80)
REVERT: C  304 LYS cc_start: 0.7604 (mtmm) cc_final: 0.7160 (mtmt)
REVERT: D   48 TYR cc_start: 0.0293 (OUTLIER) cc_final: -0.1165 (m-10)
REVERT: D  102 ASN cc_start: 0.5743 (p0) cc_final: 0.5426 (p0)
REVERT: D  110 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7037 (mtm180)
REVERT: D  255 PHE cc_start: 0.6135 (OUTLIER) cc_final: 0.5552 (m-80)
REVERT: E   48 TYR cc_start: 0.0292 (OUTLIER) cc_final: -0.1397 (m-80)
REVERT: E  110 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7147 (mtt180)
REVERT: E  255 PHE cc_start: 0.5952 (OUTLIER) cc_final: 0.5153 (m-80)
  outliers start: 64
  outliers final: 44
  residues processed: 198
  average time/residue: 0.1230
  time to fit residues: 35.6612
Evaluate side-chains
  203 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 145
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
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  128 SER
Chi-restraints excluded: chain A residue  181 TRP
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  242 VAL
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  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  234 LEU
Chi-restraints excluded: chain B residue  242 VAL
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  172 GLN
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  234 LEU
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   53 ARG
Chi-restraints excluded: chain D residue   61 VAL
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  181 TRP
Chi-restraints excluded: chain D residue  191 THR
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  234 LEU
Chi-restraints excluded: chain D residue  255 PHE
Chi-restraints excluded: chain E residue   48 TYR
Chi-restraints excluded: chain E residue   53 ARG
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  218 LEU
Chi-restraints excluded: chain E residue  242 VAL
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 129 optimal weight:    9.9990
   chunk 64 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 150 optimal weight:   10.0000
   chunk 97 optimal weight:    0.5980
   chunk 153 optimal weight:   10.0000
   chunk 98 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0670
   chunk 80 optimal weight:    4.9990
   chunk 83 optimal weight:    0.4980
   chunk 114 optimal weight:    5.9990
   overall best weight:    2.0322

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.236638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.207035 restraints weight = 13237.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.4234 rms_B_bonded: 1.00
r_work: 0.3896 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3575 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.2942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  13580  Z= 0.219
  Angle     :  0.738  11.093  18520  Z= 0.352
  Chirality :  0.048   0.233   2185
  Planarity :  0.004   0.030   2235
  Dihedral  :  7.971  44.361   2270
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  3.40 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 32.94 %
    Favored  : 62.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.12 (0.22), residues: 1560
  helix:  2.52 (0.24), residues: 500
  sheet: -0.73 (0.24), residues: 335
  loop : -1.70 (0.23), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 138 
 TYR   0.009   0.001   TYR C 433 
 PHE   0.030   0.002   PHE B  99 
 TRP   0.018   0.002   TRP B 261 
 HIS   0.005   0.001   HIS E 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00510 (13545)
  covalent geometry    : angle       0.71996 (18435)
  SS BOND              : bond        0.00715 (    5)
  SS BOND              : angle       3.14935 (   10)
  hydrogen bonds       : bond        0.03790 (  625)
  hydrogen bonds       : angle       4.14642 ( 2220)
  Misc. bond           : bond        0.00095 (    5)
  link_ALPHA1-4        : bond        0.00823 (    5)
  link_ALPHA1-4        : angle       3.27560 (   15)
  link_BETA1-4         : bond        0.00524 (   10)
  link_BETA1-4         : angle       2.59388 (   30)
  link_NAG-ASN         : bond        0.00187 (   10)
  link_NAG-ASN         : angle       1.59454 (   30)

********************** 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
  205 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 143
  time to evaluate  : 0.551 
Fit side-chains
REVERT: A   48 TYR cc_start: -0.0330 (OUTLIER) cc_final: -0.1976 (m-80)
REVERT: A  234 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8058 (tp)
REVERT: A  255 PHE cc_start: 0.6414 (OUTLIER) cc_final: 0.5964 (m-80)
REVERT: A  318 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7237 (p90)
REVERT: B   48 TYR cc_start: -0.0002 (OUTLIER) cc_final: -0.1672 (m-80)
REVERT: B  102 ASN cc_start: 0.6093 (p0) cc_final: 0.5627 (p0)
REVERT: B  110 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7232 (mtm180)
REVERT: B  197 ASP cc_start: 0.6897 (p0) cc_final: 0.6679 (t0)
REVERT: B  250 TYR cc_start: 0.7052 (m-80) cc_final: 0.6677 (m-80)
REVERT: B  304 LYS cc_start: 0.7461 (mtmm) cc_final: 0.6860 (mtmt)
REVERT: C   48 TYR cc_start: 0.0197 (OUTLIER) cc_final: -0.2262 (m-80)
REVERT: C  102 ASN cc_start: 0.6044 (p0) cc_final: 0.5651 (p0)
REVERT: C  110 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7443 (mtm180)
REVERT: C  255 PHE cc_start: 0.5919 (OUTLIER) cc_final: 0.5172 (m-80)
REVERT: D   48 TYR cc_start: -0.0093 (OUTLIER) cc_final: -0.1336 (m-10)
REVERT: D  102 ASN cc_start: 0.5850 (p0) cc_final: 0.5452 (p0)
REVERT: D  110 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7269 (mtm180)
REVERT: D  250 TYR cc_start: 0.7045 (m-80) cc_final: 0.6711 (m-80)
REVERT: D  255 PHE cc_start: 0.6106 (OUTLIER) cc_final: 0.5563 (m-80)
REVERT: E   48 TYR cc_start: 0.0027 (OUTLIER) cc_final: -0.1529 (m-80)
REVERT: E  110 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7369 (mtt180)
REVERT: E  255 PHE cc_start: 0.6008 (OUTLIER) cc_final: 0.5272 (m-80)
  outliers start: 62
  outliers final: 42
  residues processed: 192
  average time/residue: 0.1195
  time to fit residues: 33.9524
Evaluate side-chains
  194 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 137
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
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  110 ARG
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  181 TRP
Chi-restraints excluded: chain A residue  218 LEU
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  110 ARG
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  169 MET
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  234 LEU
Chi-restraints excluded: chain B residue  242 VAL
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  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   53 ARG
Chi-restraints excluded: chain D residue   61 VAL
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  181 TRP
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  211 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  181 TRP
Chi-restraints excluded: chain E residue  205 LEU
Chi-restraints excluded: chain E residue  218 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 150 optimal weight:    0.8980
   chunk 113 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 101 optimal weight:    0.7980
   chunk 43 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9980
   chunk 31 optimal weight:    8.9990
   chunk 82 optimal weight:    9.9990
   chunk 42 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.8780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4515 r_free = 0.4515 target = 0.238715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.209872 restraints weight = 13255.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.4273 rms_B_bonded: 0.98
r_work: 0.3959 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.3655 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.2932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13580  Z= 0.142
  Angle     :  0.671  11.074  18520  Z= 0.318
  Chirality :  0.045   0.221   2185
  Planarity :  0.003   0.029   2235
  Dihedral  :  7.619  43.137   2270
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  2.50 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 33.36 %
    Favored  : 62.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.03 (0.22), residues: 1560
  helix:  2.54 (0.24), residues: 500
  sheet: -0.59 (0.24), residues: 335
  loop : -1.55 (0.23), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  91 
 TYR   0.013   0.001   TYR C 433 
 PHE   0.029   0.002   PHE B  99 
 TRP   0.019   0.002   TRP B 261 
 HIS   0.005   0.001   HIS E 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (13545)
  covalent geometry    : angle       0.65452 (18435)
  SS BOND              : bond        0.00531 (    5)
  SS BOND              : angle       2.37579 (   10)
  hydrogen bonds       : bond        0.03578 (  625)
  hydrogen bonds       : angle       3.85903 ( 2220)
  Misc. bond           : bond        0.00069 (    5)
  link_ALPHA1-4        : bond        0.01156 (    5)
  link_ALPHA1-4        : angle       2.36892 (   15)
  link_BETA1-4         : bond        0.00591 (   10)
  link_BETA1-4         : angle       2.73940 (   30)
  link_NAG-ASN         : bond        0.00187 (   10)
  link_NAG-ASN         : angle       1.54407 (   30)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3190.23 seconds
wall clock time: 55 minutes 39.55 seconds (3339.55 seconds total)