Starting phenix.real_space_refine
on Thu Aug  6 03:05:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9wso_66201/08_2026/9wso_66201_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9wso_66201/08_2026/9wso_66201.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.45
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9wso_66201/08_2026/9wso_66201_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9wso_66201/08_2026/9wso_66201_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9wso_66201/08_2026/9wso_66201.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9wso_66201/08_2026/9wso_66201.map"
  }
  resolution = 3.45
  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=   0.000 sd=   0.045
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      56      5.16       5
     C    8062      2.51       5
     N    2180      2.21       5
     O    2494      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12792
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3360
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 422, 3360
          Classifications: {'peptide': 422}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 412}
    Chain: "B"
      Number of atoms: 3360
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 422, 3360
          Classifications: {'peptide': 422}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 412}
    Chain: "C"
      Number of atoms: 1356
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 180, 1356
          Classifications: {'peptide': 180}
          Link IDs: {'PTRANS': 5, 'TRANS': 174}
    Chain: "D"
      Number of atoms: 3360
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 422, 3360
          Classifications: {'peptide': 422}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 412}
    Chain: "O"
      Number of atoms: 1356
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 180, 1356
          Classifications: {'peptide': 180}
          Link IDs: {'PTRANS': 5, 'TRANS': 174}
  Time building chain proxies: 2.71, per 1000 atoms: 0.21
  Number of scatterers: 12792
  At special positions: 0
  Unit cell: (83.916, 96.348, 124.32, 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      56     16.00
     O    2494      8.00
     N    2180      7.00
     C    8062      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  38 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  38 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  38 " distance=2.04

  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=0, symmetry=0
  Time building additional restraints: 0.81
  Conformation dependent library (CDL) restraints added in 383.6 milliseconds
  

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2876

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 16 sheets defined
      2.3% alpha, 54.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 159 through 163
    Processing helix  chain 'A' and resid 239 through 241
      No H-bonds generated for 'chain 'A' and resid 239 through 241'
    Processing helix  chain 'A' and resid 397 through 401
      removed outlier: 3.638A  pdb=" N   GLY A 400 " --> pdb=" O   ASP A 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 163
      removed outlier: 3.858A  pdb=" N   ASP B 162 " --> pdb=" O   ASN B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 397 through 401
      removed outlier: 3.957A  pdb=" N   GLY B 400 " --> pdb=" O   ASP B 397 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 113 through 116
    Processing helix  chain 'D' and resid 159 through 163
    Processing helix  chain 'O' and resid 49 through 53
    Processing sheet with id=AA1, first strand: chain 'A' and resid 203 through 204
      removed outlier: 4.203A  pdb=" N   GLY A 150 " --> pdb=" O   ASN A 165 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ASN A 165 " --> pdb=" O   GLY A 150 " (cutoff:3.500A)
      removed outlier: 5.425A  pdb=" N   ASN A 169 " --> pdb=" O   ASN A 197 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   ASN A 197 " --> pdb=" O   ASN A 169 " (cutoff:3.500A)
      removed outlier: 5.553A  pdb=" N   VAL A 171 " --> pdb=" O   ARG A 195 " (cutoff:3.500A)
      removed outlier: 7.471A  pdb=" N   ARG A 195 " --> pdb=" O   VAL A 171 " (cutoff:3.500A)
      removed outlier: 5.580A  pdb=" N   ASP A 173 " --> pdb=" O   TYR A 193 " (cutoff:3.500A)
      removed outlier: 7.405A  pdb=" N   TYR A 193 " --> pdb=" O   ASP A 173 " (cutoff:3.500A)
      removed outlier: 5.372A  pdb=" N   ARG A 175 " --> pdb=" O   VAL A 191 " (cutoff:3.500A)
      removed outlier: 7.290A  pdb=" N   VAL A 191 " --> pdb=" O   ARG A 175 " (cutoff:3.500A)
      removed outlier: 4.860A  pdb=" N   ALA A 177 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   LEU A 189 " --> pdb=" O   ALA A 177 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ILE A 181 " --> pdb=" O   GLY A 185 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   GLY A 185 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   GLY A 267 " --> pdb=" O   ASP A 237 " (cutoff:3.500A)
      removed outlier: 5.526A  pdb=" N   TRP A 305 " --> pdb=" O   GLU A 332 " (cutoff:3.500A)
      removed outlier: 7.390A  pdb=" N   GLU A 332 " --> pdb=" O   TRP A 305 " (cutoff:3.500A)
      removed outlier: 5.492A  pdb=" N   THR A 307 " --> pdb=" O   ASN A 330 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   ASN A 330 " --> pdb=" O   THR A 307 " (cutoff:3.500A)
      removed outlier: 5.376A  pdb=" N   GLY A 309 " --> pdb=" O   TYR A 328 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   TYR A 328 " --> pdb=" O   GLY A 309 " (cutoff:3.500A)
      removed outlier: 5.487A  pdb=" N   ARG A 311 " --> pdb=" O   ILE A 326 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   ILE A 326 " --> pdb=" O   ARG A 311 " (cutoff:3.500A)
      removed outlier: 5.381A  pdb=" N   MET A 313 " --> pdb=" O   MET A 324 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   MET A 324 " --> pdb=" O   MET A 313 " (cutoff:3.500A)
      removed outlier: 5.549A  pdb=" N   LYS A 315 " --> pdb=" O   THR A 322 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   THR A 322 " --> pdb=" O   LYS A 315 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   TRP A 421 " --> pdb=" O   GLY A   5 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   GLY A   5 " --> pdb=" O   TRP A 421 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   LEU A  46 " --> pdb=" O   THR A  62 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   THR A  62 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   PHE A  58 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   LYS A  52 " --> pdb=" O   LYS A  56 " (cutoff:3.500A)
      removed outlier: 7.128A  pdb=" N   LYS A  56 " --> pdb=" O   LYS A  52 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   SER A  57 " --> pdb=" O   GLY A  88 " (cutoff:3.500A)
      removed outlier: 4.582A  pdb=" N   GLY A  88 " --> pdb=" O   SER A  57 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   TYR A  59 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   VAL A  86 " --> pdb=" O   TYR A  59 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ASP A  61 " --> pdb=" O   ALA A  84 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   ALA A  84 " --> pdb=" O   ASP A  61 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   ASN A  63 " --> pdb=" O   ARG A  82 " (cutoff:3.500A)
      removed outlier: 11.623A  pdb=" N   GLY A 124 " --> pdb=" O   SER A 147 " (cutoff:3.500A)
      removed outlier: 10.561A  pdb=" N   SER A 147 " --> pdb=" O   GLY A 124 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   GLY A 126 " --> pdb=" O   ARG A 145 " (cutoff:3.500A)
      removed outlier: 7.252A  pdb=" N   ARG A 145 " --> pdb=" O   GLY A 126 " (cutoff:3.500A)
      removed outlier: 5.131A  pdb=" N   GLY A 128 " --> pdb=" O   ALA A 143 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   ALA A 143 " --> pdb=" O   GLY A 128 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   GLU A 130 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   LEU A 141 " --> pdb=" O   GLU A 130 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 112
      removed outlier: 3.744A  pdb=" N   TRP A 120 " --> pdb=" O   HIS A 110 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   VAL A 112 " --> pdb=" O   TYR A 118 " (cutoff:3.500A)
      removed outlier: 5.644A  pdb=" N   TYR A 118 " --> pdb=" O   VAL A 112 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 252 through 254
    Processing sheet with id=AA4, first strand: chain 'A' and resid 376 through 378
    Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 14
      removed outlier: 3.719A  pdb=" N   LEU B  46 " --> pdb=" O   THR B  62 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   THR B  62 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   PHE B  58 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   LYS B  52 " --> pdb=" O   LYS B  56 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   LYS B  56 " --> pdb=" O   LYS B  52 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   ALA B  65 " --> pdb=" O   PHE B  81 " (cutoff:3.500A)
      removed outlier: 5.613A  pdb=" N   PHE B  81 " --> pdb=" O   ALA B  65 " (cutoff:3.500A)
      removed outlier: 11.564A  pdb=" N   GLY B 124 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 10.576A  pdb=" N   SER B 147 " --> pdb=" O   GLY B 124 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   GLY B 126 " --> pdb=" O   ARG B 145 " (cutoff:3.500A)
      removed outlier: 7.303A  pdb=" N   ARG B 145 " --> pdb=" O   GLY B 126 " (cutoff:3.500A)
      removed outlier: 5.360A  pdb=" N   GLY B 128 " --> pdb=" O   ALA B 143 " (cutoff:3.500A)
      removed outlier: 7.183A  pdb=" N   ALA B 143 " --> pdb=" O   GLY B 128 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   GLU B 130 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   LEU B 141 " --> pdb=" O   GLU B 130 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   GLY B 150 " --> pdb=" O   ASN B 165 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   ASN B 165 " --> pdb=" O   GLY B 150 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ALA B 168 " --> pdb=" O   ASN B 197 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLN B 178 " --> pdb=" O   LEU B 187 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   LEU B 187 " --> pdb=" O   GLN B 178 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   GLU B 180 " --> pdb=" O   GLY B 185 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   GLY B 185 " --> pdb=" O   GLU B 180 " (cutoff:3.500A)
      removed outlier: 5.055A  pdb=" N   GLY B 267 " --> pdb=" O   ASP B 237 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 112
      removed outlier: 6.567A  pdb=" N   HIS B 110 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 252 through 254
    Processing sheet with id=AA8, first strand: chain 'B' and resid 376 through 378
    Processing sheet with id=AA9, first strand: chain 'C' and resid 28 through 39
      removed outlier: 3.514A  pdb=" N   LYS C  56 " --> pdb=" O   ALA C  80 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ALA C  74 " --> pdb=" O   TYR C  62 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 99 through 105
    current: chain 'C' and resid 118 through 121
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 118 through 121
    current: chain 'C' and resid 160 through 161
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 160 through 161
    current: chain 'C' and resid 180 through 188
      removed outlier: 4.150A  pdb=" N   THR C 195 " --> pdb=" O   SER C 188 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 86 through 88
      removed outlier: 3.581A  pdb=" N   VAL C  87 " --> pdb=" O   HIS C  95 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 138 through 144
      removed outlier: 4.333A  pdb=" N   ILE C 143 " --> pdb=" O   TYR C 147 " (cutoff:3.500A)
      removed outlier: 7.414A  pdb=" N   TYR C 147 " --> pdb=" O   ILE C 143 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 2 through 14
      removed outlier: 3.997A  pdb=" N   LEU D  46 " --> pdb=" O   THR D  62 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   THR D  62 " --> pdb=" O   LEU D  46 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   PHE D  58 " --> pdb=" O   VAL D  50 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   LYS D  52 " --> pdb=" O   LYS D  56 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   LYS D  56 " --> pdb=" O   LYS D  52 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   ALA D  65 " --> pdb=" O   PHE D  81 " (cutoff:3.500A)
      removed outlier: 5.574A  pdb=" N   PHE D  81 " --> pdb=" O   ALA D  65 " (cutoff:3.500A)
      removed outlier: 11.639A  pdb=" N   GLY D 124 " --> pdb=" O   SER D 147 " (cutoff:3.500A)
      removed outlier: 10.566A  pdb=" N   SER D 147 " --> pdb=" O   GLY D 124 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   GLY D 126 " --> pdb=" O   ARG D 145 " (cutoff:3.500A)
      removed outlier: 7.258A  pdb=" N   ARG D 145 " --> pdb=" O   GLY D 126 " (cutoff:3.500A)
      removed outlier: 5.184A  pdb=" N   GLY D 128 " --> pdb=" O   ALA D 143 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   ALA D 143 " --> pdb=" O   GLY D 128 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   GLU D 130 " --> pdb=" O   LEU D 141 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   LEU D 141 " --> pdb=" O   GLU D 130 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   ALA D 168 " --> pdb=" O   ASN D 197 " (cutoff:3.500A)
      removed outlier: 5.817A  pdb=" N   LEU D 187 " --> pdb=" O   GLN D 178 " (cutoff:3.500A)
      removed outlier: 4.893A  pdb=" N   GLU D 180 " --> pdb=" O   GLY D 185 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   GLY D 185 " --> pdb=" O   GLU D 180 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   GLY D 267 " --> pdb=" O   ASP D 237 " (cutoff:3.500A)
      removed outlier: 5.534A  pdb=" N   TRP D 305 " --> pdb=" O   GLU D 332 " (cutoff:3.500A)
      removed outlier: 7.515A  pdb=" N   GLU D 332 " --> pdb=" O   TRP D 305 " (cutoff:3.500A)
      removed outlier: 5.618A  pdb=" N   THR D 307 " --> pdb=" O   ASN D 330 " (cutoff:3.500A)
      removed outlier: 7.601A  pdb=" N   ASN D 330 " --> pdb=" O   THR D 307 " (cutoff:3.500A)
      removed outlier: 5.376A  pdb=" N   GLY D 309 " --> pdb=" O   TYR D 328 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   TYR D 328 " --> pdb=" O   GLY D 309 " (cutoff:3.500A)
      removed outlier: 5.372A  pdb=" N   ARG D 311 " --> pdb=" O   ILE D 326 " (cutoff:3.500A)
      removed outlier: 7.446A  pdb=" N   ILE D 326 " --> pdb=" O   ARG D 311 " (cutoff:3.500A)
      removed outlier: 5.365A  pdb=" N   MET D 313 " --> pdb=" O   MET D 324 " (cutoff:3.500A)
      removed outlier: 7.275A  pdb=" N   MET D 324 " --> pdb=" O   MET D 313 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   LYS D 315 " --> pdb=" O   THR D 322 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   THR D 322 " --> pdb=" O   LYS D 315 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   LEU D 347 " --> pdb=" O   ALA D 367 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   TRP D 421 " --> pdb=" O   GLY D   5 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   GLY D   5 " --> pdb=" O   TRP D 421 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 110 through 112
      removed outlier: 6.910A  pdb=" N   HIS D 110 " --> pdb=" O   TYR D 119 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   TYR D 119 " --> pdb=" O   HIS D 110 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 252 through 254
    Processing sheet with id=AB6, first strand: chain 'D' and resid 376 through 378
    Processing sheet with id=AB7, first strand: chain 'O' and resid 28 through 38
      removed outlier: 3.529A  pdb=" N   VAL O  72 " --> pdb=" O   TYR O  64 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'O' and resid 72 through 76
    current: chain 'O' and resid 95 through 103
  WARNING: can't find start of bonding for strands!
    previous: chain 'O' and resid 95 through 103
    current: chain 'O' and resid 119 through 144
      removed outlier: 6.747A  pdb=" N   ARG O 139 " --> pdb=" O   THR O 152 " (cutoff:3.500A)
      removed outlier: 5.493A  pdb=" N   THR O 152 " --> pdb=" O   ARG O 139 " (cutoff:3.500A)
      removed outlier: 7.929A  pdb=" N   THR O 141 " --> pdb=" O   GLU O 150 " (cutoff:3.500A)
      removed outlier: 5.892A  pdb=" N   GLU O 150 " --> pdb=" O   THR O 141 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   ILE O 143 " --> pdb=" O   MET O 148 " (cutoff:3.500A)
      removed outlier: 7.914A  pdb=" N   MET O 148 " --> pdb=" O   ILE O 143 " (cutoff:3.500A)

    609 hydrogen bonds defined for protein.
    1677 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: 2.13

  Time building geometry restraints manager: 1.13 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4206
        1.34 -     1.46: 3401
        1.46 -     1.58: 5423
        1.58 -     1.70: 0
        1.70 -     1.82: 106
  Bond restraints: 13136
  Sorted by residual:
  bond pdb=" CA  SER D 238 "
       pdb=" C   SER D 238 "
    ideal  model  delta    sigma   weight residual
    1.524  1.483  0.041 2.25e-02 1.98e+03 3.30e+00
  bond pdb=" CB  THR A  40 "
       pdb=" CG2 THR A  40 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.49e+00
  bond pdb=" C   GLY D 124 "
       pdb=" N   PRO D 125 "
    ideal  model  delta    sigma   weight residual
    1.335  1.322  0.013 8.70e-03 1.32e+04 2.38e+00
  bond pdb=" CB  ASN A 340 "
       pdb=" CG  ASN A 340 "
    ideal  model  delta    sigma   weight residual
    1.516  1.480  0.036 2.50e-02 1.60e+03 2.04e+00
  bond pdb=" CB  THR B  40 "
       pdb=" CG2 THR B  40 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 3.30e-02 9.18e+02 1.88e+00
  ... (remaining 13131 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.12: 17682
        3.12 -     6.24: 120
        6.24 -     9.36: 5
        9.36 -    12.47: 1
       12.47 -    15.59: 1
  Bond angle restraints: 17809
  Sorted by residual:
  angle pdb=" N   LYS B 210 "
        pdb=" CA  LYS B 210 "
        pdb=" CB  LYS B 210 "
      ideal   model   delta    sigma   weight residual
     114.17  109.10    5.07 1.14e+00 7.69e-01 1.98e+01
  angle pdb=" C   THR C  41 "
        pdb=" N   LEU C  42 "
        pdb=" CA  LEU C  42 "
      ideal   model   delta    sigma   weight residual
     121.95  137.54  -15.59 3.74e+00 7.15e-02 1.74e+01
  angle pdb=" N   GLY O  47 "
        pdb=" CA  GLY O  47 "
        pdb=" C   GLY O  47 "
      ideal   model   delta    sigma   weight residual
     113.18  121.58   -8.40 2.37e+00 1.78e-01 1.26e+01
  angle pdb=" N   GLY O  48 "
        pdb=" CA  GLY O  48 "
        pdb=" C   GLY O  48 "
      ideal   model   delta    sigma   weight residual
     113.18  121.27   -8.09 2.37e+00 1.78e-01 1.17e+01
  angle pdb=" N   ASP D 397 "
        pdb=" CA  ASP D 397 "
        pdb=" C   ASP D 397 "
      ideal   model   delta    sigma   weight residual
     110.80  104.25    6.55 2.13e+00 2.20e-01 9.45e+00
  ... (remaining 17804 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.64: 6332
       17.64 -    35.29: 887
       35.29 -    52.93: 189
       52.93 -    70.57: 46
       70.57 -    88.21: 16
  Dihedral angle restraints: 7470
    sinusoidal: 2884
      harmonic: 4586
  Sorted by residual:
  dihedral pdb=" CA  TYR A  32 "
           pdb=" C   TYR A  32 "
           pdb=" N   ARG A  33 "
           pdb=" CA  ARG A  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.70  -22.30     0      5.00e+00 4.00e-02 1.99e+01
  dihedral pdb=" CA  LEU O  42 "
           pdb=" C   LEU O  42 "
           pdb=" N   PRO O  43 "
           pdb=" CA  PRO O  43 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.87  -19.13     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  TRP D 420 "
           pdb=" C   TRP D 420 "
           pdb=" N   TRP D 421 "
           pdb=" CA  TRP D 421 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.06  -18.94     0      5.00e+00 4.00e-02 1.44e+01
  ... (remaining 7467 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1507
       0.068 -    0.136: 262
       0.136 -    0.204: 13
       0.204 -    0.272: 0
       0.272 -    0.341: 1
  Chirality restraints: 1783
  Sorted by residual:
  chirality pdb=" CB  VAL C 106 "
            pdb=" CA  VAL C 106 "
            pdb=" CG1 VAL C 106 "
            pdb=" CG2 VAL C 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.29   -0.34 2.00e-01 2.50e+01 2.90e+00
  chirality pdb=" CB  ILE B 263 "
            pdb=" CA  ILE B 263 "
            pdb=" CG1 ILE B 263 "
            pdb=" CG2 ILE B 263 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.09e-01
  chirality pdb=" CB  ILE D 263 "
            pdb=" CA  ILE D 263 "
            pdb=" CG1 ILE D 263 "
            pdb=" CG2 ILE D 263 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.65e-01
  ... (remaining 1780 not shown)

  Planarity restraints: 2331
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 421 "    0.030 2.00e-02 2.50e+03   2.57e-02 1.66e+01
        pdb=" CG  TRP D 421 "   -0.066 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 421 "    0.035 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 421 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 421 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 421 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 421 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 421 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 421 "    0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 421 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP D 397 "   -0.012 2.00e-02 2.50e+03   2.48e-02 6.13e+00
        pdb=" CG  ASP D 397 "    0.043 2.00e-02 2.50e+03
        pdb=" OD1 ASP D 397 "   -0.016 2.00e-02 2.50e+03
        pdb=" OD2 ASP D 397 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 317 "    0.037 5.00e-02 4.00e+02   5.49e-02 4.82e+00
        pdb=" N   PRO D 318 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO D 318 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO D 318 "    0.030 5.00e-02 4.00e+02
  ... (remaining 2328 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 333
        2.67 -     3.23: 11403
        3.23 -     3.78: 19272
        3.78 -     4.34: 26501
        4.34 -     4.90: 47550
  Nonbonded interactions: 105059
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 170 "
            pdb=" ND2 ASN A 197 "
     model   vdw
     2.110 3.120
  nonbonded pdb=" O   LEU A  95 "
            pdb=" OG  SER A  98 "
     model   vdw
     2.126 3.040
  nonbonded pdb=" O   LEU D  95 "
            pdb=" OG  SER D  98 "
     model   vdw
     2.142 3.040
  nonbonded pdb=" OD1 ASP A 285 "
            pdb=" NZ  LYS A 315 "
     model   vdw
     2.182 3.120
  nonbonded pdb=" NZ  LYS C  61 "
            pdb=" OD2 ASP C 182 "
     model   vdw
     2.185 3.120
  ... (remaining 105054 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'O'
}

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:             2.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     10.950
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
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      :  0.007   0.052  13139  Z= 0.320
  Angle     :  0.758  15.594  17815  Z= 0.427
  Chirality :  0.050   0.341   1783
  Planarity :  0.005   0.055   2331
  Dihedral  : 17.411  88.213   4585
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.92 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 29.95 %
    Favored  : 69.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 are not related in a simple way.
  whole: -1.95 (0.20), residues: 1616
  helix: -4.53 (0.42), residues: 36
  sheet: -0.56 (0.17), residues: 859
  loop : -1.99 (0.20), residues: 721

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 145 
 TYR   0.020   0.002   TYR O 138 
 PHE   0.026   0.002   PHE C 198 
 TRP   0.066   0.002   TRP D 421 
 HIS   0.006   0.001   HIS O  95 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00722 /  0.32 (13136)
  covalent geometry    : angle       0.75745 /  0.43 (17809)
  SS BOND              : bond        0.00637 /  0.32 (    3)
  SS BOND              : angle       2.20745 /  1.35 (    6)
  hydrogen bonds       : bond        0.10323 /  6.93 (  609)
  hydrogen bonds       : angle       6.44357 /  4.43 ( 1677)

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 154
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 TRP cc_start: 0.6963 (p-90) cc_final: 0.6388 (m100)
  outliers start: 12
  outliers final: 10
  residues processed: 157
  average time/residue: 0.1036
  time to fit residues: 23.7632
Evaluate side-chains
  160 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 150
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ASP
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain B residue   55 ASP
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  291 MET
Chi-restraints excluded: chain C residue   27 HIS
Chi-restraints excluded: chain C residue  204 TYR
Chi-restraints excluded: chain D residue  160 ILE
Chi-restraints excluded: chain D residue  336 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    4.9990
   overall best weight:    1.7786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 340 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 = 0.3545 r_free = 0.3545 target = 0.137309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.119500 restraints weight = 14888.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 1.35
r_work: 0.2926 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.2824 rms_B_bonded: 2.62 restraints_weight: 0.2500
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8520
moved from start:          0.0648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059  13139  Z= 0.247
  Angle     :  0.633   9.524  17815  Z= 0.347
  Chirality :  0.048   0.220   1783
  Planarity :  0.004   0.059   2331
  Dihedral  :  5.929  47.344   1796
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 27.74 %
    Favored  : 68.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 are not related in a simple way.
  whole: -1.90 (0.20), residues: 1616
  helix: -4.56 (0.37), residues: 36
  sheet: -0.52 (0.17), residues: 851
  loop : -1.95 (0.20), residues: 729

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 145 
 TYR   0.021   0.002   TYR B 118 
 PHE   0.010   0.001   PHE O  30 
 TRP   0.032   0.002   TRP D 421 
 HIS   0.004   0.001   HIS O  95 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00569 /  0.25 (13136)
  covalent geometry    : angle       0.63225 /  0.35 (17809)
  SS BOND              : bond        0.00358 /  0.18 (    3)
  SS BOND              : angle       1.22476 /  0.76 (    6)
  hydrogen bonds       : bond        0.03228 /  2.11 (  609)
  hydrogen bonds       : angle       5.66613 /  3.88 ( 1677)

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 166
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 TRP cc_start: 0.7308 (p-90) cc_final: 0.5129 (p90)
REVERT: C   34 TYR cc_start: 0.8205 (t80) cc_final: 0.7849 (t80)
REVERT: C  150 GLU cc_start: 0.8252 (pm20) cc_final: 0.8030 (pm20)
REVERT: C  194 ARG cc_start: 0.8631 (ttt90) cc_final: 0.8424 (ttt-90)
REVERT: D  118 TYR cc_start: 0.9038 (m-80) cc_final: 0.8792 (m-80)
REVERT: O  173 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8324 (mt)
  outliers start: 53
  outliers final: 28
  residues processed: 203
  average time/residue: 0.0944
  time to fit residues: 28.3166
Evaluate side-chains
  184 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 155
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  179 MET
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  247 SER
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain C residue   73 MET
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  196 ASP
Chi-restraints excluded: chain C residue  204 TYR
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue  216 THR
Chi-restraints excluded: chain D residue  256 ASN
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain D residue  368 THR
Chi-restraints excluded: chain O residue   45 LEU
Chi-restraints excluded: chain O residue  173 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 87 optimal weight:    0.5980
   chunk 72 optimal weight:    4.9990
   chunk 117 optimal weight:    7.9990
   chunk 35 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 130 optimal weight:    0.3980
   chunk 147 optimal weight:    2.9990
   overall best weight:    1.3986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  71 GLN
D 340 ASN
O  54 HIS
O  95 HIS
O 174 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.138515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.120740 restraints weight = 14885.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3014 rms_B_bonded: 1.36
r_work: 0.2937 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.2833 rms_B_bonded: 2.64 restraints_weight: 0.2500
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.0854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  13139  Z= 0.201
  Angle     :  0.595   9.117  17815  Z= 0.328
  Chirality :  0.047   0.236   1783
  Planarity :  0.004   0.061   2331
  Dihedral  :  5.639  50.975   1783
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 27.97 %
    Favored  : 67.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 are not related in a simple way.
  whole: -1.81 (0.20), residues: 1616
  helix: -4.46 (0.43), residues: 36
  sheet: -0.46 (0.17), residues: 851
  loop : -1.89 (0.21), residues: 729

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 145 
 TYR   0.016   0.002   TYR B 118 
 PHE   0.009   0.001   PHE B 259 
 TRP   0.027   0.001   TRP D 421 
 HIS   0.003   0.001   HIS O  95 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00462 /  0.20 (13136)
  covalent geometry    : angle       0.59480 /  0.33 (17809)
  SS BOND              : bond        0.00415 /  0.21 (    3)
  SS BOND              : angle       1.16209 /  0.73 (    6)
  hydrogen bonds       : bond        0.02960 /  1.92 (  609)
  hydrogen bonds       : angle       5.49906 /  3.76 ( 1677)

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 164
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 TRP cc_start: 0.7250 (p-90) cc_final: 0.5149 (p90)
REVERT: C   34 TYR cc_start: 0.8211 (t80) cc_final: 0.7836 (t80)
REVERT: C  150 GLU cc_start: 0.8204 (pm20) cc_final: 0.7981 (pm20)
REVERT: D  340 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.8120 (p0)
REVERT: O  139 ARG cc_start: 0.8237 (ptm-80) cc_final: 0.8005 (ptm-80)
REVERT: O  173 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8379 (mt)
  outliers start: 62
  outliers final: 37
  residues processed: 206
  average time/residue: 0.0815
  time to fit residues: 25.3048
Evaluate side-chains
  190 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 151
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  179 MET
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain C residue   27 HIS
Chi-restraints excluded: chain C residue   73 MET
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  173 ILE
Chi-restraints excluded: chain C residue  204 TYR
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain D residue  216 THR
Chi-restraints excluded: chain D residue  256 ASN
Chi-restraints excluded: chain D residue  340 ASN
Chi-restraints excluded: chain D residue  346 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain D residue  368 THR
Chi-restraints excluded: chain D residue  412 THR
Chi-restraints excluded: chain O residue   31 THR
Chi-restraints excluded: chain O residue   45 LEU
Chi-restraints excluded: chain O residue  135 THR
Chi-restraints excluded: chain O residue  173 ILE
Chi-restraints excluded: chain O residue  174 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 139 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 99 optimal weight:    0.0000
   chunk 55 optimal weight:    0.0970
   chunk 143 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.9786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  72 ASN
** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  21 GLN
** B  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 340 ASN
O 174 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.139646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.121574 restraints weight = 14806.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.3030 rms_B_bonded: 1.39
r_work: 0.2953 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.2847 rms_B_bonded: 2.72 restraints_weight: 0.2500
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.1039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13139  Z= 0.152
  Angle     :  0.567   8.593  17815  Z= 0.310
  Chirality :  0.046   0.242   1783
  Planarity :  0.004   0.060   2331
  Dihedral  :  5.524  54.301   1783
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 28.51 %
    Favored  : 66.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 are not related in a simple way.
  whole: -1.69 (0.20), residues: 1616
  helix: -4.39 (0.49), residues: 36
  sheet: -0.36 (0.17), residues: 857
  loop : -1.85 (0.21), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 145 
 TYR   0.012   0.001   TYR B 118 
 PHE   0.007   0.001   PHE B 259 
 TRP   0.023   0.001   TRP D 421 
 HIS   0.002   0.000   HIS D 275 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.15 (13136)
  covalent geometry    : angle       0.56674 /  0.31 (17809)
  SS BOND              : bond        0.00451 /  0.23 (    3)
  SS BOND              : angle       1.14328 /  0.72 (    6)
  hydrogen bonds       : bond        0.02691 /  1.74 (  609)
  hydrogen bonds       : angle       5.36631 /  3.67 ( 1677)

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 165
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 TRP cc_start: 0.7217 (p-90) cc_final: 0.5036 (p90)
REVERT: B  239 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8199 (mmm)
REVERT: C  150 GLU cc_start: 0.8190 (pm20) cc_final: 0.7916 (pm20)
REVERT: D  130 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7874 (pt0)
REVERT: D  340 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.7967 (p0)
REVERT: O  139 ARG cc_start: 0.8234 (ptm-80) cc_final: 0.8012 (ptm-80)
  outliers start: 62
  outliers final: 44
  residues processed: 204
  average time/residue: 0.0876
  time to fit residues: 27.1461
Evaluate side-chains
  203 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 156
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue  179 MET
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  417 MET
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  239 MET
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  280 MET
Chi-restraints excluded: chain C residue   27 HIS
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain C residue   73 MET
Chi-restraints excluded: chain C residue  107 MET
Chi-restraints excluded: chain C residue  173 ILE
Chi-restraints excluded: chain C residue  204 TYR
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue  130 GLU
Chi-restraints excluded: chain D residue  160 ILE
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain D residue  197 ASN
Chi-restraints excluded: chain D residue  216 THR
Chi-restraints excluded: chain D residue  256 ASN
Chi-restraints excluded: chain D residue  340 ASN
Chi-restraints excluded: chain D residue  346 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain D residue  368 THR
Chi-restraints excluded: chain O residue   31 THR
Chi-restraints excluded: chain O residue   45 LEU
Chi-restraints excluded: chain O residue   93 THR
Chi-restraints excluded: chain O residue  135 THR
Chi-restraints excluded: chain O residue  174 ASN
Chi-restraints excluded: chain O residue  196 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 102 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 140 optimal weight:    0.6980
   chunk 73 optimal weight:    2.9990
   chunk 157 optimal weight:   20.0000
   chunk 117 optimal weight:    7.9990
   chunk 43 optimal weight:    0.8980
   chunk 32 optimal weight:    0.5980
   chunk 39 optimal weight:    0.0870
   chunk 27 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9980
   overall best weight:    0.6158

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 340 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 = 0.3598 r_free = 0.3598 target = 0.141741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.124166 restraints weight = 14764.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 1.34
r_work: 0.2981 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 2.61 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.1270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  13139  Z= 0.116
  Angle     :  0.541   8.429  17815  Z= 0.297
  Chirality :  0.045   0.253   1783
  Planarity :  0.004   0.058   2331
  Dihedral  :  5.235  56.271   1781
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 28.35 %
    Favored  : 66.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 are not related in a simple way.
  whole: -1.59 (0.20), residues: 1616
  helix: -4.36 (0.52), residues: 36
  sheet: -0.26 (0.18), residues: 854
  loop : -1.82 (0.21), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  33 
 TYR   0.016   0.001   TYR C  34 
 PHE   0.007   0.001   PHE B 227 
 TRP   0.021   0.001   TRP D 421 
 HIS   0.001   0.000   HIS D 275 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.12 (13136)
  covalent geometry    : angle       0.54085 /  0.30 (17809)
  SS BOND              : bond        0.00456 /  0.24 (    3)
  SS BOND              : angle       1.27031 /  0.82 (    6)
  hydrogen bonds       : bond        0.02480 /  1.60 (  609)
  hydrogen bonds       : angle       5.25804 /  3.58 ( 1677)

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 164
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 THR cc_start: 0.8309 (t) cc_final: 0.8066 (t)
REVERT: A   94 TRP cc_start: 0.7238 (p-90) cc_final: 0.5185 (p90)
REVERT: B   40 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8226 (t)
REVERT: C  150 GLU cc_start: 0.8088 (pm20) cc_final: 0.7866 (pm20)
REVERT: D  188 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7215 (tm-30)
REVERT: O  139 ARG cc_start: 0.8269 (ptm-80) cc_final: 0.8048 (ptm-80)
  outliers start: 62
  outliers final: 44
  residues processed: 205
  average time/residue: 0.0930
  time to fit residues: 28.4084
Evaluate side-chains
  200 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 154
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  179 MET
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  417 MET
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  280 MET
Chi-restraints excluded: chain B residue  408 SER
Chi-restraints excluded: chain C residue   27 HIS
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain C residue   73 MET
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  107 MET
Chi-restraints excluded: chain C residue  173 ILE
Chi-restraints excluded: chain C residue  204 TYR
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain D residue  188 GLU
Chi-restraints excluded: chain D residue  197 ASN
Chi-restraints excluded: chain D residue  256 ASN
Chi-restraints excluded: chain D residue  346 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain D residue  368 THR
Chi-restraints excluded: chain D residue  412 THR
Chi-restraints excluded: chain O residue   31 THR
Chi-restraints excluded: chain O residue   70 VAL
Chi-restraints excluded: chain O residue   87 VAL
Chi-restraints excluded: chain O residue   93 THR
Chi-restraints excluded: chain O residue  112 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 85 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 110 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 340 ASN
O 174 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.138665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.121182 restraints weight = 14830.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3023 rms_B_bonded: 1.32
r_work: 0.2948 rms_B_bonded: 1.52 restraints_weight: 0.5000
r_work: 0.2846 rms_B_bonded: 2.57 restraints_weight: 0.2500
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.1177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  13139  Z= 0.192
  Angle     :  0.580   8.457  17815  Z= 0.317
  Chirality :  0.046   0.275   1783
  Planarity :  0.004   0.060   2331
  Dihedral  :  5.389  58.936   1781
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 28.12 %
    Favored  : 66.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 are not related in a simple way.
  whole: -1.56 (0.20), residues: 1616
  helix: -4.33 (0.55), residues: 36
  sheet: -0.26 (0.18), residues: 854
  loop : -1.79 (0.21), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  33 
 TYR   0.016   0.002   TYR C  34 
 PHE   0.009   0.001   PHE B 259 
 TRP   0.025   0.001   TRP D 421 
 HIS   0.003   0.001   HIS D 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00444 /  0.19 (13136)
  covalent geometry    : angle       0.57910 /  0.32 (17809)
  SS BOND              : bond        0.00456 /  0.23 (    3)
  SS BOND              : angle       1.38520 /  0.87 (    6)
  hydrogen bonds       : bond        0.02812 /  1.81 (  609)
  hydrogen bonds       : angle       5.30429 /  3.62 ( 1677)

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 160
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 THR cc_start: 0.8255 (t) cc_final: 0.7945 (t)
REVERT: A   94 TRP cc_start: 0.7176 (p-90) cc_final: 0.5211 (p90)
REVERT: B   40 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8291 (t)
REVERT: B  239 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8197 (mmm)
REVERT: C  150 GLU cc_start: 0.8081 (pm20) cc_final: 0.7832 (pm20)
REVERT: D  188 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.7293 (tm-30)
REVERT: D  340 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8025 (p0)
  outliers start: 68
  outliers final: 51
  residues processed: 209
  average time/residue: 0.0948
  time to fit residues: 29.9978
Evaluate side-chains
  213 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 158
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  179 MET
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  239 MET
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  280 MET
Chi-restraints excluded: chain B residue  319 ILE
Chi-restraints excluded: chain B residue  408 SER
Chi-restraints excluded: chain C residue   27 HIS
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain C residue   73 MET
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  107 MET
Chi-restraints excluded: chain C residue  173 ILE
Chi-restraints excluded: chain C residue  204 TYR
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain D residue  188 GLU
Chi-restraints excluded: chain D residue  197 ASN
Chi-restraints excluded: chain D residue  216 THR
Chi-restraints excluded: chain D residue  256 ASN
Chi-restraints excluded: chain D residue  340 ASN
Chi-restraints excluded: chain D residue  346 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain D residue  368 THR
Chi-restraints excluded: chain D residue  412 THR
Chi-restraints excluded: chain O residue   31 THR
Chi-restraints excluded: chain O residue   70 VAL
Chi-restraints excluded: chain O residue   87 VAL
Chi-restraints excluded: chain O residue   93 THR
Chi-restraints excluded: chain O residue  135 THR
Chi-restraints excluded: chain O residue  143 ILE
Chi-restraints excluded: chain O residue  174 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 149 optimal weight:    2.9990
   chunk 129 optimal weight:    2.9990
   chunk 155 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9990
   chunk 76 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 117 optimal weight:    7.9990
   chunk 93 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 69 optimal weight:    2.9990
   chunk 161 optimal weight:    0.8980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  20 GLN
D 340 ASN
O  54 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.140841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.123249 restraints weight = 14715.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 1.33
r_work: 0.2970 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.2868 rms_B_bonded: 2.59 restraints_weight: 0.2500
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.1318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  13139  Z= 0.137
  Angle     :  0.554   8.387  17815  Z= 0.302
  Chirality :  0.046   0.280   1783
  Planarity :  0.004   0.060   2331
  Dihedral  :  5.258  55.825   1781
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 29.12 %
    Favored  : 66.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 are not related in a simple way.
  whole: -1.47 (0.20), residues: 1616
  helix: -4.36 (0.52), residues: 36
  sheet: -0.18 (0.18), residues: 854
  loop : -1.75 (0.21), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG O 102 
 TYR   0.011   0.001   TYR B 118 
 PHE   0.008   0.001   PHE D 259 
 TRP   0.026   0.001   TRP D 421 
 HIS   0.002   0.000   HIS D 275 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.14 (13136)
  covalent geometry    : angle       0.55320 /  0.30 (17809)
  SS BOND              : bond        0.00383 /  0.19 (    3)
  SS BOND              : angle       1.21628 /  0.77 (    6)
  hydrogen bonds       : bond        0.02532 /  1.62 (  609)
  hydrogen bonds       : angle       5.22863 /  3.57 ( 1677)

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 161
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 THR cc_start: 0.8187 (t) cc_final: 0.7835 (t)
REVERT: A   94 TRP cc_start: 0.7258 (p-90) cc_final: 0.5232 (p90)
REVERT: B   40 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8276 (t)
REVERT: C  150 GLU cc_start: 0.8083 (pm20) cc_final: 0.7843 (pm20)
REVERT: C  204 TYR cc_start: 0.7819 (OUTLIER) cc_final: 0.6884 (p90)
REVERT: D  188 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7261 (tm-30)
REVERT: D  340 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.7997 (p0)
  outliers start: 60
  outliers final: 45
  residues processed: 202
  average time/residue: 0.0885
  time to fit residues: 27.0448
Evaluate side-chains
  206 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 157
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  179 MET
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  280 MET
Chi-restraints excluded: chain B residue  319 ILE
Chi-restraints excluded: chain B residue  408 SER
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain C residue   73 MET
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  107 MET
Chi-restraints excluded: chain C residue  173 ILE
Chi-restraints excluded: chain C residue  204 TYR
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain D residue  188 GLU
Chi-restraints excluded: chain D residue  197 ASN
Chi-restraints excluded: chain D residue  216 THR
Chi-restraints excluded: chain D residue  256 ASN
Chi-restraints excluded: chain D residue  340 ASN
Chi-restraints excluded: chain D residue  346 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain D residue  368 THR
Chi-restraints excluded: chain D residue  412 THR
Chi-restraints excluded: chain O residue   31 THR
Chi-restraints excluded: chain O residue   70 VAL
Chi-restraints excluded: chain O residue   87 VAL
Chi-restraints excluded: chain O residue  135 THR
Chi-restraints excluded: chain O residue  143 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 96 optimal weight:    0.8980
   chunk 124 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 128 optimal weight:    5.9990
   chunk 98 optimal weight:    7.9990
   chunk 46 optimal weight:    0.7980
   chunk 135 optimal weight:    5.9990
   chunk 90 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   overall best weight:    1.9184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.136563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.118958 restraints weight = 14824.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 1.33
r_work: 0.2924 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.2822 rms_B_bonded: 2.58 restraints_weight: 0.2500
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.1154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066  13139  Z= 0.259
  Angle     :  0.628   8.542  17815  Z= 0.344
  Chirality :  0.048   0.311   1783
  Planarity :  0.004   0.061   2331
  Dihedral  :  5.527  52.335   1781
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.06 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 29.04 %
    Favored  : 65.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 are not related in a simple way.
  whole: -1.56 (0.20), residues: 1616
  helix: -4.35 (0.54), residues: 36
  sheet: -0.27 (0.18), residues: 845
  loop : -1.76 (0.21), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG O 102 
 TYR   0.020   0.002   TYR B 118 
 PHE   0.013   0.001   PHE D 259 
 TRP   0.034   0.002   TRP D 421 
 HIS   0.002   0.001   HIS D 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00600 /  0.26 (13136)
  covalent geometry    : angle       0.62701 /  0.34 (17809)
  SS BOND              : bond        0.00586 /  0.29 (    3)
  SS BOND              : angle       1.58573 /  0.99 (    6)
  hydrogen bonds       : bond        0.03092 /  1.99 (  609)
  hydrogen bonds       : angle       5.39024 /  3.69 ( 1677)

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 158
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 THR cc_start: 0.8405 (t) cc_final: 0.8005 (t)
REVERT: A   94 TRP cc_start: 0.7193 (p-90) cc_final: 0.5361 (p90)
REVERT: B   40 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.8341 (t)
REVERT: B  116 ASP cc_start: 0.8518 (t0) cc_final: 0.8286 (t70)
REVERT: C   34 TYR cc_start: 0.8191 (t80) cc_final: 0.7851 (t80)
REVERT: C  150 GLU cc_start: 0.8143 (pm20) cc_final: 0.7895 (pm20)
REVERT: C  204 TYR cc_start: 0.7956 (OUTLIER) cc_final: 0.7057 (p90)
REVERT: D  188 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.7320 (tm-30)
REVERT: D  340 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.8067 (p0)
REVERT: D  399 ASN cc_start: 0.8374 (p0) cc_final: 0.8139 (p0)
  outliers start: 66
  outliers final: 54
  residues processed: 208
  average time/residue: 0.0841
  time to fit residues: 26.5246
Evaluate side-chains
  213 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 155
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  179 MET
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  282 ASP
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  280 MET
Chi-restraints excluded: chain B residue  319 ILE
Chi-restraints excluded: chain B residue  408 SER
Chi-restraints excluded: chain B residue  417 MET
Chi-restraints excluded: chain B residue  419 ILE
Chi-restraints excluded: chain C residue   27 HIS
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain C residue   73 MET
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  107 MET
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  173 ILE
Chi-restraints excluded: chain C residue  204 TYR
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain D residue  188 GLU
Chi-restraints excluded: chain D residue  197 ASN
Chi-restraints excluded: chain D residue  216 THR
Chi-restraints excluded: chain D residue  256 ASN
Chi-restraints excluded: chain D residue  340 ASN
Chi-restraints excluded: chain D residue  346 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain D residue  368 THR
Chi-restraints excluded: chain D residue  412 THR
Chi-restraints excluded: chain O residue   31 THR
Chi-restraints excluded: chain O residue   70 VAL
Chi-restraints excluded: chain O residue   87 VAL
Chi-restraints excluded: chain O residue  135 THR
Chi-restraints excluded: chain O residue  143 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 116 optimal weight:    3.9990
   chunk 68 optimal weight:    5.9990
   chunk 118 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 94 optimal weight:    5.9990
   chunk 80 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 106 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    2.1586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  21 GLN
D 340 ASN
O  54 HIS
O 174 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.141289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.122174 restraints weight = 15030.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 1.74
r_work: 0.3387 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3258 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8647
moved from start:          0.1152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.073  13139  Z= 0.289
  Angle     :  0.659   8.528  17815  Z= 0.360
  Chirality :  0.049   0.324   1783
  Planarity :  0.004   0.061   2331
  Dihedral  :  5.661  58.207   1781
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 28.81 %
    Favored  : 66.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 are not related in a simple way.
  whole: -1.64 (0.20), residues: 1616
  helix: -4.42 (0.50), residues: 36
  sheet: -0.33 (0.18), residues: 845
  loop : -1.79 (0.21), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG O 102 
 TYR   0.021   0.002   TYR B 118 
 PHE   0.016   0.002   PHE D 259 
 TRP   0.042   0.002   TRP D 421 
 HIS   0.002   0.001   HIS D 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00671 /  0.29 (13136)
  covalent geometry    : angle       0.65693 /  0.36 (17809)
  SS BOND              : bond        0.00875 /  0.44 (    3)
  SS BOND              : angle       2.60500 /  1.68 (    6)
  hydrogen bonds       : bond        0.03261 /  2.11 (  609)
  hydrogen bonds       : angle       5.47692 /  3.76 ( 1677)

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 155
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 THR cc_start: 0.8507 (t) cc_final: 0.8063 (t)
REVERT: A   94 TRP cc_start: 0.7130 (p-90) cc_final: 0.5329 (p90)
REVERT: B   40 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8466 (t)
REVERT: C   34 TYR cc_start: 0.8237 (t80) cc_final: 0.7902 (t80)
REVERT: C  150 GLU cc_start: 0.8177 (pm20) cc_final: 0.7942 (pm20)
REVERT: C  204 TYR cc_start: 0.8187 (OUTLIER) cc_final: 0.7409 (p90)
REVERT: D   21 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7592 (mp10)
REVERT: D  188 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.7396 (tm-30)
REVERT: D  340 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8237 (p0)
REVERT: D  399 ASN cc_start: 0.8374 (p0) cc_final: 0.8126 (p0)
REVERT: D  421 TRP cc_start: 0.8588 (p90) cc_final: 0.8319 (p90)
  outliers start: 66
  outliers final: 55
  residues processed: 207
  average time/residue: 0.0973
  time to fit residues: 30.1114
Evaluate side-chains
  212 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 152
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  179 MET
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  282 ASP
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  280 MET
Chi-restraints excluded: chain B residue  408 SER
Chi-restraints excluded: chain B residue  417 MET
Chi-restraints excluded: chain B residue  419 ILE
Chi-restraints excluded: chain C residue   27 HIS
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain C residue   73 MET
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  107 MET
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  173 ILE
Chi-restraints excluded: chain C residue  204 TYR
Chi-restraints excluded: chain D residue   21 GLN
Chi-restraints excluded: chain D residue   55 ASP
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain D residue  188 GLU
Chi-restraints excluded: chain D residue  197 ASN
Chi-restraints excluded: chain D residue  216 THR
Chi-restraints excluded: chain D residue  256 ASN
Chi-restraints excluded: chain D residue  340 ASN
Chi-restraints excluded: chain D residue  346 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain D residue  368 THR
Chi-restraints excluded: chain D residue  412 THR
Chi-restraints excluded: chain O residue   31 THR
Chi-restraints excluded: chain O residue   70 VAL
Chi-restraints excluded: chain O residue   87 VAL
Chi-restraints excluded: chain O residue  135 THR
Chi-restraints excluded: chain O residue  143 ILE
Chi-restraints excluded: chain O residue  174 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 140 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 129 optimal weight:    1.9990
   chunk 136 optimal weight:    1.9990
   chunk 141 optimal weight:    0.7980
   chunk 102 optimal weight:    2.9990
   chunk 145 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 149 optimal weight:    3.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  71 GLN
** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 340 ASN
O 174 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.137989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.120273 restraints weight = 14851.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 1.35
r_work: 0.2936 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.2832 rms_B_bonded: 2.64 restraints_weight: 0.2500
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.1214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  13139  Z= 0.197
  Angle     :  0.610   8.496  17815  Z= 0.334
  Chirality :  0.047   0.322   1783
  Planarity :  0.004   0.061   2331
  Dihedral  :  5.532  59.389   1781
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 28.96 %
    Favored  : 66.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 are not related in a simple way.
  whole: -1.59 (0.20), residues: 1616
  helix: -4.38 (0.53), residues: 36
  sheet: -0.30 (0.18), residues: 851
  loop : -1.76 (0.21), residues: 729

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  33 
 TYR   0.016   0.002   TYR B 118 
 PHE   0.014   0.001   PHE D 259 
 TRP   0.038   0.001   TRP D 421 
 HIS   0.002   0.001   HIS D 275 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00454 /  0.20 (13136)
  covalent geometry    : angle       0.60847 /  0.33 (17809)
  SS BOND              : bond        0.00601 /  0.30 (    3)
  SS BOND              : angle       2.25786 /  1.46 (    6)
  hydrogen bonds       : bond        0.02856 /  1.83 (  609)
  hydrogen bonds       : angle       5.38860 /  3.69 ( 1677)

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 156
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 THR cc_start: 0.8349 (t) cc_final: 0.7970 (t)
REVERT: A   94 TRP cc_start: 0.7181 (p-90) cc_final: 0.5296 (p90)
REVERT: B   40 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8280 (t)
REVERT: C   34 TYR cc_start: 0.8143 (t80) cc_final: 0.7806 (t80)
REVERT: C  150 GLU cc_start: 0.8105 (pm20) cc_final: 0.7882 (pm20)
REVERT: C  204 TYR cc_start: 0.8153 (OUTLIER) cc_final: 0.7454 (p90)
REVERT: D   32 TYR cc_start: 0.8372 (m-80) cc_final: 0.7924 (m-80)
REVERT: D  188 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.7271 (tm-30)
REVERT: D  340 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.8091 (p0)
REVERT: D  399 ASN cc_start: 0.8332 (p0) cc_final: 0.8093 (p0)
REVERT: D  421 TRP cc_start: 0.8593 (p90) cc_final: 0.8374 (p90)
  outliers start: 60
  outliers final: 52
  residues processed: 204
  average time/residue: 0.1006
  time to fit residues: 31.0961
Evaluate side-chains
  210 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 154
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  179 MET
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  282 ASP
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  280 MET
Chi-restraints excluded: chain B residue  408 SER
Chi-restraints excluded: chain C residue   27 HIS
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   73 MET
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  107 MET
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  173 ILE
Chi-restraints excluded: chain C residue  204 TYR
Chi-restraints excluded: chain D residue   55 ASP
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain D residue  188 GLU
Chi-restraints excluded: chain D residue  197 ASN
Chi-restraints excluded: chain D residue  216 THR
Chi-restraints excluded: chain D residue  256 ASN
Chi-restraints excluded: chain D residue  340 ASN
Chi-restraints excluded: chain D residue  346 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain D residue  368 THR
Chi-restraints excluded: chain D residue  412 THR
Chi-restraints excluded: chain O residue   31 THR
Chi-restraints excluded: chain O residue   70 VAL
Chi-restraints excluded: chain O residue   87 VAL
Chi-restraints excluded: chain O residue  135 THR
Chi-restraints excluded: chain O residue  143 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 139 optimal weight:    0.8980
   chunk 152 optimal weight:    5.9990
   chunk 69 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   chunk 102 optimal weight:    3.9990
   chunk 43 optimal weight:    0.6980
   chunk 161 optimal weight:    5.9990
   chunk 96 optimal weight:    5.9990
   chunk 156 optimal weight:    3.9990
   chunk 84 optimal weight:    1.9990
   overall best weight:    1.9186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  21 GLN
D 340 ASN
O  54 HIS
O 174 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.136562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.118814 restraints weight = 14979.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 1.35
r_work: 0.3276 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 2.80 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
moved from start:          0.1205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064  13139  Z= 0.261
  Angle     :  0.642   8.537  17815  Z= 0.351
  Chirality :  0.048   0.179   1783
  Planarity :  0.004   0.061   2331
  Dihedral  :  5.596  57.391   1781
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 28.89 %
    Favored  : 66.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 are not related in a simple way.
  whole: -1.65 (0.20), residues: 1616
  helix: -4.44 (0.49), residues: 36
  sheet: -0.35 (0.18), residues: 851
  loop : -1.79 (0.21), residues: 729

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  33 
 TYR   0.019   0.002   TYR B 118 
 PHE   0.016   0.001   PHE D 259 
 TRP   0.038   0.002   TRP D 421 
 HIS   0.002   0.001   HIS C  54 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00604 /  0.26 (13136)
  covalent geometry    : angle       0.64090 /  0.35 (17809)
  SS BOND              : bond        0.00645 /  0.31 (    3)
  SS BOND              : angle       2.39354 /  1.53 (    6)
  hydrogen bonds       : bond        0.03122 /  2.01 (  609)
  hydrogen bonds       : angle       5.44629 /  3.74 ( 1677)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2379.86 seconds
wall clock time: 41 minutes 45.69 seconds (2505.69 seconds total)