Starting phenix.real_space_refine
on Thu Aug  6 04:42:06 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ujv_64227/08_2026/9ujv_64227.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ujv_64227/08_2026/9ujv_64227.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ujv_64227/08_2026/9ujv_64227.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ujv_64227/08_2026/9ujv_64227.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ujv_64227/08_2026/9ujv_64227.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ujv_64227/08_2026/9ujv_64227.map"
  }
  resolution = 3.86
  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=   0.001 sd=   0.026
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    8357      2.51       5
     N    2308      2.21       5
     O    2442      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s

  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: 13163
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1542
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1542
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 9, 'TRANS': 185}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2342
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 295, 2342
          Classifications: {'peptide': 295}
          Link IDs: {'PTRANS': 11, 'TRANS': 283}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 297, 2358
          Classifications: {'peptide': 297}
          Link IDs: {'PTRANS': 12, 'TRANS': 284}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 297, 2358
          Classifications: {'peptide': 297}
          Link IDs: {'PTRANS': 12, 'TRANS': 284}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 2358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 297, 2358
          Classifications: {'peptide': 297}
          Link IDs: {'PTRANS': 11, 'TRANS': 285}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 2205
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2205
          Classifications: {'peptide': 277}
          Link IDs: {'PTRANS': 11, 'TRANS': 265}
          Chain breaks: 2
  Time building chain proxies: 2.79, per 1000 atoms: 0.21
  Number of scatterers: 13163
  At special positions: 0
  Unit cell: (94.928, 127.734, 128.432, 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    2442      8.00
     N    2308      7.00
     C    8357      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        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: 1.08
  Conformation dependent library (CDL) restraints added in 608.2 milliseconds
  

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3146

  Finding SS restraints...
    Secondary structure from input PDB file:
      71 helices and 17 sheets defined
      47.5% alpha, 13.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 23
    Processing helix  chain 'A' and resid 53 through 64
      removed outlier: 3.563A  pdb=" N   ASN A  64 " --> pdb=" O   GLY A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 89
      removed outlier: 4.197A  pdb=" N   HIS A  80 " --> pdb=" O   GLY A  76 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ILE A  81 " --> pdb=" O   LYS A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 107
    Processing helix  chain 'A' and resid 126 through 133
    Processing helix  chain 'A' and resid 143 through 146
    Processing helix  chain 'A' and resid 153 through 160
      removed outlier: 4.125A  pdb=" N   VAL A 157 " --> pdb=" O   VAL A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 211
      removed outlier: 3.883A  pdb=" N   TRP A 211 " --> pdb=" O   GLN A 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 22
    Processing helix  chain 'B' and resid 50 through 64
    Processing helix  chain 'B' and resid 76 through 89
    Processing helix  chain 'B' and resid 102 through 107
    Processing helix  chain 'B' and resid 126 through 133
      removed outlier: 3.620A  pdb=" N   TRP B 130 " --> pdb=" O   GLY B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 160
      removed outlier: 3.636A  pdb=" N   SER B 160 " --> pdb=" O   ARG B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 209
    Processing helix  chain 'B' and resid 221 through 233
    Processing helix  chain 'B' and resid 240 through 262
      removed outlier: 3.786A  pdb=" N   ILE B 244 " --> pdb=" O   GLU B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 284
      removed outlier: 3.602A  pdb=" N   ALA B 281 " --> pdb=" O   ALA B 277 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   ILE B 282 " --> pdb=" O   GLU B 278 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 285 through 294
    Processing helix  chain 'B' and resid 295 through 298
    Processing helix  chain 'B' and resid 299 through 315
      removed outlier: 3.887A  pdb=" N   ALA B 304 " --> pdb=" O   GLU B 300 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   THR B 305 " --> pdb=" O   LEU B 301 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 18 through 23
      removed outlier: 3.569A  pdb=" N   GLY C  23 " --> pdb=" O   ARG C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 50 through 64
      removed outlier: 3.530A  pdb=" N   ASN C  64 " --> pdb=" O   GLY C  60 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 89
      removed outlier: 3.814A  pdb=" N   ILE C  81 " --> pdb=" O   LYS C  77 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 107
      removed outlier: 3.749A  pdb=" N   LEU C 106 " --> pdb=" O   SER C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 126 through 134
    Processing helix  chain 'C' and resid 147 through 159
      removed outlier: 4.455A  pdb=" N   VAL C 153 " --> pdb=" O   ASP C 149 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 221 through 231
      removed outlier: 3.693A  pdb=" N   ASN C 227 " --> pdb=" O   ASP C 223 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE C 228 " --> pdb=" O   ASN C 224 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 238 through 262
      removed outlier: 3.636A  pdb=" N   GLU C 243 " --> pdb=" O   ALA C 239 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   ILE C 244 " --> pdb=" O   GLU C 240 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ALA C 252 " --> pdb=" O   MET C 248 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   ALA C 258 " --> pdb=" O   MET C 254 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   PHE C 259 " --> pdb=" O   THR C 255 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ILE C 260 " --> pdb=" O   ARG C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 269 through 284
      removed outlier: 3.993A  pdb=" N   ALA C 281 " --> pdb=" O   ALA C 277 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 287 through 294
      removed outlier: 4.064A  pdb=" N   ARG C 291 " --> pdb=" O   GLY C 287 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU C 292 " --> pdb=" O   PHE C 288 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 299 through 315
      removed outlier: 4.207A  pdb=" N   ALA C 304 " --> pdb=" O   GLU C 300 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   THR C 305 " --> pdb=" O   LEU C 301 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 17 through 23
      removed outlier: 3.707A  pdb=" N   VAL D  21 " --> pdb=" O   SER D  17 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 63
    Processing helix  chain 'D' and resid 76 through 89
      removed outlier: 3.635A  pdb=" N   HIS D  80 " --> pdb=" O   GLY D  76 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ILE D  81 " --> pdb=" O   LYS D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 102 through 106
      removed outlier: 4.114A  pdb=" N   LEU D 106 " --> pdb=" O   ARG D 103 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 126 through 134
      removed outlier: 3.883A  pdb=" N   TRP D 130 " --> pdb=" O   GLY D 126 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 149 through 159
      removed outlier: 4.609A  pdb=" N   VAL D 153 " --> pdb=" O   ASP D 149 " (cutoff:3.500A)
      removed outlier: 4.945A  pdb=" N   GLN D 155 " --> pdb=" O   MET D 151 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   VAL D 157 " --> pdb=" O   VAL D 153 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 206 through 211
    Processing helix  chain 'D' and resid 221 through 233
    Processing helix  chain 'D' and resid 234 through 237
    Processing helix  chain 'D' and resid 238 through 261
      removed outlier: 3.957A  pdb=" N   GLU D 243 " --> pdb=" O   ALA D 239 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ILE D 244 " --> pdb=" O   GLU D 240 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 269 through 284
    Processing helix  chain 'D' and resid 285 through 294
      removed outlier: 3.692A  pdb=" N   PHE D 290 " --> pdb=" O   VAL D 286 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ARG D 291 " --> pdb=" O   GLY D 287 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 299 through 315
      removed outlier: 4.171A  pdb=" N   ALA D 304 " --> pdb=" O   GLU D 300 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   THR D 305 " --> pdb=" O   LEU D 301 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   VAL D 306 " --> pdb=" O   GLU D 302 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 18 through 23
    Processing helix  chain 'E' and resid 50 through 64
    Processing helix  chain 'E' and resid 76 through 89
    Processing helix  chain 'E' and resid 102 through 107
    Processing helix  chain 'E' and resid 126 through 134
    Processing helix  chain 'E' and resid 147 through 160
      removed outlier: 4.106A  pdb=" N   PHE E 152 " --> pdb=" O   PRO E 148 " (cutoff:3.500A)
      removed outlier: 5.579A  pdb=" N   VAL E 153 " --> pdb=" O   ASP E 149 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ILE E 154 " --> pdb=" O   VAL E 150 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 207 through 211
    Processing helix  chain 'E' and resid 221 through 233
      removed outlier: 3.728A  pdb=" N   LYS E 232 " --> pdb=" O   ILE E 228 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 239 through 261
      removed outlier: 4.360A  pdb=" N   GLU E 243 " --> pdb=" O   ALA E 239 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   ILE E 244 " --> pdb=" O   GLU E 240 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 269 through 284
    Processing helix  chain 'E' and resid 285 through 294
    Processing helix  chain 'E' and resid 295 through 298
    Processing helix  chain 'E' and resid 299 through 314
      removed outlier: 4.102A  pdb=" N   ALA E 304 " --> pdb=" O   GLU E 300 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   THR E 305 " --> pdb=" O   LEU E 301 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 18 through 23
    Processing helix  chain 'F' and resid 56 through 63
    Processing helix  chain 'F' and resid 76 through 88
    Processing helix  chain 'F' and resid 102 through 108
    Processing helix  chain 'F' and resid 126 through 134
    Processing helix  chain 'F' and resid 149 through 159
      removed outlier: 4.222A  pdb=" N   ARG F 156 " --> pdb=" O   PHE F 152 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   VAL F 157 " --> pdb=" O   VAL F 153 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   GLU F 159 " --> pdb=" O   GLN F 155 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 207 through 211
    Processing helix  chain 'F' and resid 221 through 232
    Processing helix  chain 'F' and resid 240 through 261
      removed outlier: 4.346A  pdb=" N   ILE F 244 " --> pdb=" O   GLU F 240 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 269 through 284
    Processing helix  chain 'F' and resid 286 through 294
    Processing helix  chain 'F' and resid 295 through 298
    Processing helix  chain 'F' and resid 299 through 315
      removed outlier: 4.043A  pdb=" N   ALA F 304 " --> pdb=" O   GLU F 300 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   THR F 305 " --> pdb=" O   LEU F 301 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 17
    Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 96
      removed outlier: 6.430A  pdb=" N   VAL A  93 " --> pdb=" O   VAL A 139 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   ASP A 141 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   VAL A  95 " --> pdb=" O   ASP A 141 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   VAL A  67 " --> pdb=" O   ALA A 183 " (cutoff:3.500A)
      removed outlier: 7.691A  pdb=" N   ALA A 185 " --> pdb=" O   VAL A  67 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   VAL A  69 " --> pdb=" O   ALA A 185 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   MET A  68 " --> pdb=" O   THR A 215 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 115
    Processing sheet with id=AA4, first strand: chain 'B' and resid 14 through 17
    Processing sheet with id=AA5, first strand: chain 'B' and resid 92 through 96
      removed outlier: 6.138A  pdb=" N   LEU B 138 " --> pdb=" O   PHE B 182 " (cutoff:3.500A)
      removed outlier: 7.708A  pdb=" N   THR B 184 " --> pdb=" O   LEU B 138 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   PHE B 140 " --> pdb=" O   THR B 184 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   VAL B  67 " --> pdb=" O   LEU B 181 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   MET B  68 " --> pdb=" O   THR B 215 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   LEU B 217 " --> pdb=" O   MET B  68 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   SER B  70 " --> pdb=" O   LEU B 217 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 108 through 114
    Processing sheet with id=AA7, first strand: chain 'C' and resid 14 through 17
    Processing sheet with id=AA8, first strand: chain 'C' and resid 92 through 96
      removed outlier: 6.151A  pdb=" N   LEU C 138 " --> pdb=" O   PHE C 182 " (cutoff:3.500A)
      removed outlier: 7.752A  pdb=" N   THR C 184 " --> pdb=" O   LEU C 138 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   PHE C 140 " --> pdb=" O   THR C 184 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   VAL C  67 " --> pdb=" O   LEU C 181 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   MET C  68 " --> pdb=" O   THR C 215 " (cutoff:3.500A)
      removed outlier: 7.622A  pdb=" N   LEU C 217 " --> pdb=" O   MET C  68 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   SER C  70 " --> pdb=" O   LEU C 217 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 108 through 114
    Processing sheet with id=AB1, first strand: chain 'D' and resid 14 through 16
    Processing sheet with id=AB2, first strand: chain 'D' and resid 92 through 96
      removed outlier: 3.882A  pdb=" N   VAL D  67 " --> pdb=" O   LEU D 181 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 108 through 114
    Processing sheet with id=AB4, first strand: chain 'E' and resid 14 through 17
    Processing sheet with id=AB5, first strand: chain 'E' and resid 92 through 96
      removed outlier: 6.342A  pdb=" N   LEU E 138 " --> pdb=" O   PHE E 182 " (cutoff:3.500A)
      removed outlier: 7.873A  pdb=" N   THR E 184 " --> pdb=" O   LEU E 138 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   PHE E 140 " --> pdb=" O   THR E 184 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   VAL E  67 " --> pdb=" O   LEU E 181 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   MET E  68 " --> pdb=" O   THR E 215 " (cutoff:3.500A)
      removed outlier: 7.619A  pdb=" N   LEU E 217 " --> pdb=" O   MET E  68 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   SER E  70 " --> pdb=" O   LEU E 217 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 108 through 115
    Processing sheet with id=AB7, first strand: chain 'F' and resid 15 through 17
    Processing sheet with id=AB8, first strand: chain 'F' and resid 92 through 96
      removed outlier: 6.463A  pdb=" N   VAL F  67 " --> pdb=" O   ALA F 183 " (cutoff:3.500A)
      removed outlier: 7.866A  pdb=" N   ALA F 185 " --> pdb=" O   VAL F  67 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   VAL F  69 " --> pdb=" O   ALA F 185 " (cutoff:3.500A)

    564 hydrogen bonds defined for protein.
    1626 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: 1.96

  Time building geometry restraints manager: 1.42 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: 4433
        1.34 -     1.46: 3056
        1.46 -     1.58: 5851
        1.58 -     1.70: 1
        1.70 -     1.82: 101
  Bond restraints: 13442
  Sorted by residual:
  bond pdb=" N   ASN C 218 "
       pdb=" CA  ASN C 218 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.15e-02 7.56e+03 8.83e+00
  bond pdb=" N   ASN B 218 "
       pdb=" CA  ASN B 218 "
    ideal  model  delta    sigma   weight residual
    1.453  1.489 -0.036 1.27e-02 6.20e+03 7.87e+00
  bond pdb=" N   TYR C 219 "
       pdb=" CA  TYR C 219 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.035 1.27e-02 6.20e+03 7.56e+00
  bond pdb=" N   VAL F 229 "
       pdb=" CA  VAL F 229 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.17e-02 7.31e+03 7.48e+00
  bond pdb=" N   TYR B 219 "
       pdb=" CA  TYR B 219 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.29e-02 6.01e+03 6.18e+00
  ... (remaining 13437 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 18024
        2.41 -     4.82: 220
        4.82 -     7.24: 30
        7.24 -     9.65: 10
        9.65 -    12.06: 2
  Bond angle restraints: 18286
  Sorted by residual:
  angle pdb=" C   ASP F 253 "
        pdb=" N   MET F 254 "
        pdb=" CA  MET F 254 "
      ideal   model   delta    sigma   weight residual
     121.58  111.10   10.48 1.95e+00 2.63e-01 2.89e+01
  angle pdb=" CA  PRO A  31 "
        pdb=" N   PRO A  31 "
        pdb=" CD  PRO A  31 "
      ideal   model   delta    sigma   weight residual
     112.00  104.71    7.29 1.40e+00 5.10e-01 2.71e+01
  angle pdb=" CB  MET F 208 "
        pdb=" CG  MET F 208 "
        pdb=" SD  MET F 208 "
      ideal   model   delta    sigma   weight residual
     112.70  124.76  -12.06 3.00e+00 1.11e-01 1.62e+01
  angle pdb=" CB  ARG C 210 "
        pdb=" CG  ARG C 210 "
        pdb=" CD  ARG C 210 "
      ideal   model   delta    sigma   weight residual
     111.30  120.24   -8.94 2.30e+00 1.89e-01 1.51e+01
  angle pdb=" C   GLU C 159 "
        pdb=" N   SER C 160 "
        pdb=" CA  SER C 160 "
      ideal   model   delta    sigma   weight residual
     123.05  117.62    5.43 1.40e+00 5.10e-01 1.51e+01
  ... (remaining 18281 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.54: 6615
       17.54 -    35.09: 972
       35.09 -    52.63: 331
       52.63 -    70.17: 56
       70.17 -    87.71: 26
  Dihedral angle restraints: 8000
    sinusoidal: 3151
      harmonic: 4849
  Sorted by residual:
  dihedral pdb=" CA  MET D 151 "
           pdb=" C   MET D 151 "
           pdb=" N   PHE D 152 "
           pdb=" CA  PHE D 152 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.44   22.56     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" CA  TYR D  63 "
           pdb=" C   TYR D  63 "
           pdb=" N   ASN D  64 "
           pdb=" CA  ASN D  64 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.28   19.72     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  MET C  29 "
           pdb=" C   MET C  29 "
           pdb=" N   VAL C  30 "
           pdb=" CA  VAL C  30 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.29  -18.71     0      5.00e+00 4.00e-02 1.40e+01
  ... (remaining 7997 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1466
       0.041 -    0.082: 445
       0.082 -    0.123: 156
       0.123 -    0.163: 9
       0.163 -    0.204: 4
  Chirality restraints: 2080
  Sorted by residual:
  chirality pdb=" CA  MET F 254 "
            pdb=" N   MET F 254 "
            pdb=" C   MET F 254 "
            pdb=" CB  MET F 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CA  LEU E  88 "
            pdb=" N   LEU E  88 "
            pdb=" C   LEU E  88 "
            pdb=" CB  LEU E  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.87e-01
  chirality pdb=" CA  MET E 254 "
            pdb=" N   MET E 254 "
            pdb=" C   MET E 254 "
            pdb=" CB  MET E 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.02e-01
  ... (remaining 2077 not shown)

  Planarity restraints: 2381
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A  30 "   -0.084 5.00e-02 4.00e+02   1.24e-01 2.46e+01
        pdb=" N   PRO A  31 "    0.214 5.00e-02 4.00e+02
        pdb=" CA  PRO A  31 "   -0.065 5.00e-02 4.00e+02
        pdb=" CD  PRO A  31 "   -0.065 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS E 176 "    0.038 5.00e-02 4.00e+02   5.79e-02 5.36e+00
        pdb=" N   PRO E 177 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO E 177 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO E 177 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  40 "    0.038 5.00e-02 4.00e+02   5.74e-02 5.27e+00
        pdb=" N   PRO B  41 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO B  41 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B  41 "    0.032 5.00e-02 4.00e+02
  ... (remaining 2378 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1243
        2.74 -     3.28: 13153
        3.28 -     3.82: 21803
        3.82 -     4.36: 23997
        4.36 -     4.90: 41518
  Nonbonded interactions: 101714
  Sorted by model distance:
  nonbonded pdb=" O   ASN A  10 "
            pdb=" OH  TYR A  33 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" O   SER F 269 "
            pdb=" OG1 THR F 272 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" O   ALA B 289 "
            pdb=" OG1 THR B 293 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" OD1 ASP C  98 "
            pdb=" N   SER C  99 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" OD1 ASP B 141 "
            pdb=" OG1 THR B 184 "
     model   vdw
     2.225 3.040
  ... (remaining 101709 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 10 through 109 or resid 124 through 188 or resid 205 throu \ 
gh 316))
  selection = (chain 'C' and (resid 10 through 109 or resid 124 through 316))
  selection = (chain 'D' and (resid 10 through 109 or resid 124 through 316))
  selection = (chain 'E' and (resid 10 through 109 or resid 124 through 188 or resid 205 throu \ 
gh 316))
  selection = chain 'F'
}

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 group one per residue
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:             5.340
  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:          0.370
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     12.070
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7143
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.096  13442  Z= 0.167
  Angle     :  0.662  12.060  18286  Z= 0.352
  Chirality :  0.043   0.204   2080
  Planarity :  0.005   0.124   2381
  Dihedral  : 19.116  87.713   4854
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 38.50 %
    Favored  : 60.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.30 (0.21), residues: 1632
  helix:  0.53 (0.20), residues: 671
  sheet:  0.28 (0.32), residues: 260
  loop : -1.04 (0.24), residues: 701

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG C 303 
 TYR   0.019   0.001   TYR E 219 
 PHE   0.025   0.001   PHE E 290 
 TRP   0.031   0.002   TRP F 276 
 HIS   0.004   0.001   HIS F  80 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00332 /  0.17 (13442)
  covalent geometry    : angle       0.66213 /  0.35 (18286)
  hydrogen bonds       : bond        0.15127 / 10.10 (  564)
  hydrogen bonds       : angle       6.95506 /  5.02 ( 1626)

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

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

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  406 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 389
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  109 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7768 (ttmm)
REVERT: B  253 ASP cc_start: 0.7569 (m-30) cc_final: 0.7317 (m-30)
REVERT: C  243 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7287 (mm-30)
REVERT: D   94 ARG cc_start: 0.7960 (mtm110) cc_final: 0.7632 (mtp85)
REVERT: D  182 PHE cc_start: 0.7964 (m-10) cc_final: 0.7761 (m-10)
REVERT: D  299 ASP cc_start: 0.8091 (t0) cc_final: 0.7847 (t0)
REVERT: E  248 MET cc_start: 0.8243 (mmt) cc_final: 0.7714 (mmm)
REVERT: E  250 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.6778 (mpp80)
REVERT: E  268 MET cc_start: 0.7885 (tpp) cc_final: 0.7611 (tpp)
  outliers start: 17
  outliers final: 7
  residues processed: 393
  average time/residue: 0.1178
  time to fit residues: 63.8094
Evaluate side-chains
  393 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 384
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain B residue   57 ILE
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  109 LYS
Chi-restraints excluded: chain B residue  255 THR
Chi-restraints excluded: chain C residue  220 LEU
Chi-restraints excluded: chain D residue  302 GLU
Chi-restraints excluded: chain E residue  209 ASP
Chi-restraints excluded: chain E residue  250 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0770
   chunk 130 optimal weight:    0.0670
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    0.0040
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    0.0980
   chunk 149 optimal weight:    0.0050
   overall best weight:    0.0502

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 227 ASN
C 246 ASN
C 284 ASN
E  64 ASN
E 205 GLN
E 224 ASN
E 296 ASN
** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.171225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.133349 restraints weight = 21854.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.138012 restraints weight = 11718.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.141127 restraints weight = 7690.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.143298 restraints weight = 5787.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.144095 restraints weight = 4746.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
moved from start:          0.1093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  13442  Z= 0.097
  Angle     :  0.550  12.522  18286  Z= 0.279
  Chirality :  0.041   0.165   2080
  Planarity :  0.005   0.077   2381
  Dihedral  :  4.839  49.167   1844
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 33.99 %
    Favored  : 62.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.21), residues: 1632
  helix:  0.74 (0.20), residues: 670
  sheet:  0.65 (0.34), residues: 232
  loop : -0.94 (0.24), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 303 
 TYR   0.013   0.001   TYR E 219 
 PHE   0.023   0.001   PHE E 290 
 TRP   0.022   0.001   TRP F 276 
 HIS   0.005   0.001   HIS B 222 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00212 /  0.10 (13442)
  covalent geometry    : angle       0.54998 /  0.28 (18286)
  hydrogen bonds       : bond        0.03082 /  2.01 (  564)
  hydrogen bonds       : angle       5.37663 /  3.92 ( 1626)

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

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

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  456 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 408
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 ASP cc_start: 0.6119 (p0) cc_final: 0.5805 (p0)
REVERT: B  109 LYS cc_start: 0.7877 (ttmm) cc_final: 0.7663 (ttmm)
REVERT: B  253 ASP cc_start: 0.7490 (m-30) cc_final: 0.7198 (m-30)
REVERT: C   94 ARG cc_start: 0.7782 (mtp180) cc_final: 0.7493 (mtp-110)
REVERT: C  141 ASP cc_start: 0.7642 (t0) cc_final: 0.7179 (m-30)
REVERT: C  248 MET cc_start: 0.7255 (ttt) cc_final: 0.6896 (ttp)
REVERT: C  290 PHE cc_start: 0.7849 (t80) cc_final: 0.7343 (t80)
REVERT: C  302 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7768 (mp0)
REVERT: D   94 ARG cc_start: 0.8105 (mtm110) cc_final: 0.7773 (mtp85)
REVERT: D  155 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.7281 (tt0)
REVERT: D  286 VAL cc_start: 0.8554 (p) cc_final: 0.8321 (m)
REVERT: D  291 ARG cc_start: 0.7583 (mtp180) cc_final: 0.7288 (mtp85)
REVERT: E  227 ASN cc_start: 0.8130 (m-40) cc_final: 0.7866 (m110)
REVERT: E  250 ARG cc_start: 0.7527 (mtp85) cc_final: 0.6742 (mtp85)
REVERT: E  254 MET cc_start: 0.7495 (mpp) cc_final: 0.6929 (mpp)
REVERT: E  268 MET cc_start: 0.7748 (tpp) cc_final: 0.7520 (tpp)
REVERT: F  256 ARG cc_start: 0.7790 (ptp90) cc_final: 0.7572 (ptp90)
REVERT: F  268 MET cc_start: 0.7452 (mmm) cc_final: 0.7084 (mmm)
  outliers start: 48
  outliers final: 18
  residues processed: 431
  average time/residue: 0.1299
  time to fit residues: 78.0333
Evaluate side-chains
  410 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 390
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  208 MET
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain C residue  220 LEU
Chi-restraints excluded: chain C residue  251 VAL
Chi-restraints excluded: chain C residue  302 GLU
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue  150 VAL
Chi-restraints excluded: chain D residue  155 GLN
Chi-restraints excluded: chain D residue  173 ILE
Chi-restraints excluded: chain D residue  186 ASN
Chi-restraints excluded: chain D residue  295 LEU
Chi-restraints excluded: chain E residue  172 VAL
Chi-restraints excluded: chain E residue  295 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 30 optimal weight:   10.0000
   chunk 7 optimal weight:    4.9990
   chunk 2 optimal weight:    0.1980
   chunk 153 optimal weight:    0.0770
   chunk 20 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 69 optimal weight:    1.9990
   chunk 111 optimal weight:    0.9980
   overall best weight:    0.7940

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 119 GLN
B 279 ASN
C 235 HIS
E  64 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.166857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.129189 restraints weight = 21794.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.133660 restraints weight = 11697.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.136617 restraints weight = 7696.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.138593 restraints weight = 5839.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.139870 restraints weight = 4834.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7116
moved from start:          0.1291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13442  Z= 0.148
  Angle     :  0.557  12.119  18286  Z= 0.286
  Chirality :  0.042   0.179   2080
  Planarity :  0.005   0.068   2381
  Dihedral  :  4.259  52.435   1824
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 34.84 %
    Favored  : 61.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.21), residues: 1632
  helix:  0.61 (0.20), residues: 683
  sheet:  0.73 (0.35), residues: 224
  loop : -1.02 (0.23), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 303 
 TYR   0.014   0.001   TYR B  63 
 PHE   0.020   0.001   PHE F 294 
 TRP   0.015   0.002   TRP B 276 
 HIS   0.007   0.001   HIS F  80 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00336 /  0.15 (13442)
  covalent geometry    : angle       0.55682 /  0.29 (18286)
  hydrogen bonds       : bond        0.03439 /  2.24 (  564)
  hydrogen bonds       : angle       5.25836 /  3.83 ( 1626)

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

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

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  449 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 394
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 VAL cc_start: 0.8733 (t) cc_final: 0.8297 (m)
REVERT: B   98 ASP cc_start: 0.6364 (p0) cc_final: 0.5785 (p0)
REVERT: B  109 LYS cc_start: 0.7916 (ttmm) cc_final: 0.7714 (ttmm)
REVERT: B  141 ASP cc_start: 0.7531 (t0) cc_final: 0.7325 (t0)
REVERT: B  253 ASP cc_start: 0.7600 (m-30) cc_final: 0.7346 (m-30)
REVERT: C   65 ARG cc_start: 0.8531 (mtp85) cc_final: 0.8208 (mtt-85)
REVERT: C  135 ASN cc_start: 0.7984 (p0) cc_final: 0.7752 (p0)
REVERT: C  141 ASP cc_start: 0.7709 (t0) cc_final: 0.7355 (m-30)
REVERT: C  290 PHE cc_start: 0.7876 (t80) cc_final: 0.7321 (t80)
REVERT: C  302 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7788 (mt-10)
REVERT: D  132 TYR cc_start: 0.7795 (t80) cc_final: 0.7404 (t80)
REVERT: D  291 ARG cc_start: 0.7696 (mtp180) cc_final: 0.7405 (mtp85)
REVERT: E  147 ARG cc_start: 0.8094 (ttm-80) cc_final: 0.7344 (mtm-85)
REVERT: E  227 ASN cc_start: 0.8208 (m-40) cc_final: 0.7996 (m110)
REVERT: E  250 ARG cc_start: 0.7633 (mtp85) cc_final: 0.6807 (mtp85)
REVERT: E  254 MET cc_start: 0.7680 (mpp) cc_final: 0.6992 (mpp)
REVERT: F  256 ARG cc_start: 0.7878 (ptp90) cc_final: 0.7678 (ptp90)
REVERT: F  263 ASP cc_start: 0.4181 (OUTLIER) cc_final: 0.1007 (t0)
REVERT: F  268 MET cc_start: 0.7870 (mmm) cc_final: 0.7381 (mmm)
  outliers start: 55
  outliers final: 26
  residues processed: 418
  average time/residue: 0.1285
  time to fit residues: 75.2680
Evaluate side-chains
  421 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 394
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  208 MET
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  290 PHE
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain C residue   97 LEU
Chi-restraints excluded: chain C residue  220 LEU
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue  150 VAL
Chi-restraints excluded: chain D residue  173 ILE
Chi-restraints excluded: chain D residue  186 ASN
Chi-restraints excluded: chain D residue  238 ASN
Chi-restraints excluded: chain E residue   46 ASP
Chi-restraints excluded: chain E residue   58 LEU
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain E residue  172 VAL
Chi-restraints excluded: chain E residue  209 ASP
Chi-restraints excluded: chain E residue  217 LEU
Chi-restraints excluded: chain E residue  291 ARG
Chi-restraints excluded: chain E residue  295 LEU
Chi-restraints excluded: chain F residue  263 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 159 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 121 optimal weight:    0.8980
   chunk 161 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 109 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 128 optimal weight:    0.9990
   chunk 114 optimal weight:    0.7980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  80 HIS
E  64 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.166021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.127811 restraints weight = 21551.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.132385 restraints weight = 11502.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.135411 restraints weight = 7551.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.137294 restraints weight = 5741.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.138678 restraints weight = 4779.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  13442  Z= 0.163
  Angle     :  0.579  11.828  18286  Z= 0.295
  Chirality :  0.043   0.205   2080
  Planarity :  0.005   0.066   2381
  Dihedral  :  4.375  55.427   1824
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 34.34 %
    Favored  : 61.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.16 (0.21), residues: 1632
  helix:  0.57 (0.20), residues: 675
  sheet:  0.72 (0.35), residues: 224
  loop : -0.98 (0.23), residues: 733

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 303 
 TYR   0.012   0.001   TYR C 219 
 PHE   0.024   0.001   PHE F 294 
 TRP   0.019   0.002   TRP F 276 
 HIS   0.004   0.001   HIS B 222 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.16 (13442)
  covalent geometry    : angle       0.57877 /  0.29 (18286)
  hydrogen bonds       : bond        0.03402 /  2.22 (  564)
  hydrogen bonds       : angle       5.20123 /  3.79 ( 1626)

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

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

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  465 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 401
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ARG cc_start: 0.7406 (ptp-170) cc_final: 0.7100 (ptp-110)
REVERT: B   98 ASP cc_start: 0.6545 (p0) cc_final: 0.5819 (p0)
REVERT: B  141 ASP cc_start: 0.7504 (t0) cc_final: 0.7284 (t0)
REVERT: B  253 ASP cc_start: 0.7697 (m-30) cc_final: 0.7405 (m-30)
REVERT: C   65 ARG cc_start: 0.8541 (mtp85) cc_final: 0.8232 (mtt-85)
REVERT: C  135 ASN cc_start: 0.8089 (p0) cc_final: 0.7707 (p0)
REVERT: C  141 ASP cc_start: 0.7694 (t0) cc_final: 0.7398 (m-30)
REVERT: C  151 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6887 (tpp)
REVERT: C  299 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.7126 (m-30)
REVERT: D  105 ASP cc_start: 0.8121 (t0) cc_final: 0.7879 (t0)
REVERT: D  132 TYR cc_start: 0.7770 (t80) cc_final: 0.7343 (t80)
REVERT: D  217 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8032 (tp)
REVERT: D  286 VAL cc_start: 0.8677 (p) cc_final: 0.8438 (m)
REVERT: D  291 ARG cc_start: 0.7723 (mtp180) cc_final: 0.7407 (mtp85)
REVERT: D  296 ASN cc_start: 0.8737 (m110) cc_final: 0.8530 (m110)
REVERT: E  147 ARG cc_start: 0.8063 (ttm-80) cc_final: 0.7310 (mtm-85)
REVERT: E  227 ASN cc_start: 0.8233 (m-40) cc_final: 0.8020 (m110)
REVERT: E  254 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7064 (mpp)
REVERT: F  247 LYS cc_start: 0.8598 (mtmt) cc_final: 0.8372 (mtmt)
REVERT: F  256 ARG cc_start: 0.8025 (ptp90) cc_final: 0.7784 (ptp90)
REVERT: F  263 ASP cc_start: 0.4274 (OUTLIER) cc_final: 0.1115 (t0)
REVERT: F  268 MET cc_start: 0.7918 (mmm) cc_final: 0.7295 (mmm)
REVERT: F  314 PHE cc_start: 0.6524 (m-80) cc_final: 0.6275 (m-80)
  outliers start: 64
  outliers final: 35
  residues processed: 430
  average time/residue: 0.1254
  time to fit residues: 76.0058
Evaluate side-chains
  440 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 400
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   92 CYS
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  208 MET
Chi-restraints excluded: chain B residue   37 ASP
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  173 ILE
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  210 ARG
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  296 ASN
Chi-restraints excluded: chain C residue   92 CYS
Chi-restraints excluded: chain C residue  125 ASP
Chi-restraints excluded: chain C residue  151 MET
Chi-restraints excluded: chain C residue  220 LEU
Chi-restraints excluded: chain C residue  299 ASP
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  173 ILE
Chi-restraints excluded: chain D residue  186 ASN
Chi-restraints excluded: chain D residue  217 LEU
Chi-restraints excluded: chain D residue  238 ASN
Chi-restraints excluded: chain E residue   46 ASP
Chi-restraints excluded: chain E residue   58 LEU
Chi-restraints excluded: chain E residue  100 HIS
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain E residue  217 LEU
Chi-restraints excluded: chain E residue  254 MET
Chi-restraints excluded: chain E residue  264 LEU
Chi-restraints excluded: chain E residue  291 ARG
Chi-restraints excluded: chain E residue  295 LEU
Chi-restraints excluded: chain F residue  240 GLU
Chi-restraints excluded: chain F residue  263 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 109 optimal weight:    2.9990
   chunk 121 optimal weight:    6.9990
   chunk 28 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 138 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 64.5363 > 50:)
   chunk 117 optimal weight:    9.9990
   chunk 127 optimal weight:    1.9990
   chunk 125 optimal weight:    0.3980
   chunk 37 optimal weight:    0.3980
   chunk 40 optimal weight:    7.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  80 HIS
E  64 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.163992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.125723 restraints weight = 21642.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.130196 restraints weight = 11508.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.133322 restraints weight = 7584.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.135307 restraints weight = 5732.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.136680 restraints weight = 4735.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7181
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  13442  Z= 0.193
  Angle     :  0.596  11.839  18286  Z= 0.305
  Chirality :  0.044   0.275   2080
  Planarity :  0.005   0.062   2381
  Dihedral  :  4.528  58.918   1824
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 33.92 %
    Favored  : 60.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.22 (0.21), residues: 1632
  helix:  0.50 (0.20), residues: 675
  sheet:  0.73 (0.37), residues: 208
  loop : -0.96 (0.23), residues: 749

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C 303 
 TYR   0.014   0.001   TYR E 219 
 PHE   0.026   0.002   PHE F 294 
 TRP   0.019   0.002   TRP B 276 
 HIS   0.016   0.001   HIS D  80 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00435 /  0.19 (13442)
  covalent geometry    : angle       0.59596 /  0.31 (18286)
  hydrogen bonds       : bond        0.03732 /  2.44 (  564)
  hydrogen bonds       : angle       5.25449 /  3.81 ( 1626)

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

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

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  483 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 406
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ARG cc_start: 0.7368 (ptp-170) cc_final: 0.7142 (ptp-110)
REVERT: A  167 LEU cc_start: 0.5857 (OUTLIER) cc_final: 0.5585 (tp)
REVERT: B   22 PHE cc_start: 0.8164 (m-80) cc_final: 0.7844 (m-80)
REVERT: B  141 ASP cc_start: 0.7525 (t0) cc_final: 0.7318 (t0)
REVERT: B  159 GLU cc_start: 0.6196 (tm-30) cc_final: 0.5636 (tm-30)
REVERT: B  253 ASP cc_start: 0.7751 (m-30) cc_final: 0.7435 (m-30)
REVERT: C   65 ARG cc_start: 0.8565 (mtp85) cc_final: 0.8238 (mtt-85)
REVERT: C  135 ASN cc_start: 0.8131 (p0) cc_final: 0.7714 (p0)
REVERT: C  141 ASP cc_start: 0.7733 (t0) cc_final: 0.7374 (m-30)
REVERT: C  151 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.6881 (tpp)
REVERT: C  284 ASN cc_start: 0.8016 (t0) cc_final: 0.7598 (t0)
REVERT: C  290 PHE cc_start: 0.7830 (t80) cc_final: 0.7386 (t80)
REVERT: C  302 GLU cc_start: 0.8092 (mp0) cc_final: 0.7522 (mp0)
REVERT: D   30 VAL cc_start: 0.8631 (t) cc_final: 0.8342 (p)
REVERT: D   80 HIS cc_start: 0.7751 (OUTLIER) cc_final: 0.7449 (t70)
REVERT: D   94 ARG cc_start: 0.8171 (mtp-110) cc_final: 0.7717 (mtp85)
REVERT: D  105 ASP cc_start: 0.8164 (t0) cc_final: 0.7923 (t0)
REVERT: D  132 TYR cc_start: 0.7766 (t80) cc_final: 0.7331 (t80)
REVERT: D  286 VAL cc_start: 0.8714 (p) cc_final: 0.8475 (m)
REVERT: D  291 ARG cc_start: 0.7733 (mtp180) cc_final: 0.7374 (mtp85)
REVERT: E  147 ARG cc_start: 0.8078 (ttm-80) cc_final: 0.7352 (mtm-85)
REVERT: E  227 ASN cc_start: 0.8278 (m-40) cc_final: 0.8054 (m110)
REVERT: E  254 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7004 (mpp)
REVERT: E  268 MET cc_start: 0.7890 (tpp) cc_final: 0.7171 (tpp)
REVERT: F  247 LYS cc_start: 0.8651 (mtmt) cc_final: 0.8407 (mtmt)
REVERT: F  303 ARG cc_start: 0.7290 (ttm110) cc_final: 0.6895 (ttm110)
REVERT: F  314 PHE cc_start: 0.6545 (m-80) cc_final: 0.6308 (m-80)
  outliers start: 77
  outliers final: 50
  residues processed: 445
  average time/residue: 0.1311
  time to fit residues: 81.2693
Evaluate side-chains
  452 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 398
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   92 CYS
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  208 MET
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   37 ASP
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  210 ARG
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  222 HIS
Chi-restraints excluded: chain B residue  250 ARG
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  296 ASN
Chi-restraints excluded: chain C residue   92 CYS
Chi-restraints excluded: chain C residue   97 LEU
Chi-restraints excluded: chain C residue  105 ASP
Chi-restraints excluded: chain C residue  151 MET
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  220 LEU
Chi-restraints excluded: chain C residue  243 GLU
Chi-restraints excluded: chain C residue  249 VAL
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  173 ILE
Chi-restraints excluded: chain D residue  186 ASN
Chi-restraints excluded: chain D residue  222 HIS
Chi-restraints excluded: chain D residue  238 ASN
Chi-restraints excluded: chain D residue  295 LEU
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain E residue   46 ASP
Chi-restraints excluded: chain E residue   58 LEU
Chi-restraints excluded: chain E residue   78 SER
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain E residue  100 HIS
Chi-restraints excluded: chain E residue  121 THR
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain E residue  173 ILE
Chi-restraints excluded: chain E residue  209 ASP
Chi-restraints excluded: chain E residue  217 LEU
Chi-restraints excluded: chain E residue  244 ILE
Chi-restraints excluded: chain E residue  254 MET
Chi-restraints excluded: chain E residue  264 LEU
Chi-restraints excluded: chain E residue  291 ARG
Chi-restraints excluded: chain E residue  295 LEU
Chi-restraints excluded: chain F residue  240 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 112 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 124 optimal weight:    8.9990
   chunk 31 optimal weight:    0.0970
   chunk 151 optimal weight:   30.0000
   chunk 114 optimal weight:    0.8980
   chunk 139 optimal weight:    0.9990
   chunk 137 optimal weight:    3.9990
   chunk 83 optimal weight:    0.5980
   chunk 98 optimal weight:    0.8980
   chunk 89 optimal weight:    0.5980
   overall best weight:    0.6178

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  80 HIS
E  64 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.165377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.127538 restraints weight = 21663.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.131914 restraints weight = 11683.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.134887 restraints weight = 7739.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.136787 restraints weight = 5847.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.138244 restraints weight = 4875.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7147
moved from start:          0.2005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13442  Z= 0.131
  Angle     :  0.597  12.679  18286  Z= 0.299
  Chirality :  0.043   0.312   2080
  Planarity :  0.005   0.059   2381
  Dihedral  :  4.426  55.668   1824
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 35.12 %
    Favored  : 59.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.16 (0.21), residues: 1632
  helix:  0.54 (0.20), residues: 676
  sheet:  0.65 (0.37), residues: 212
  loop : -0.89 (0.23), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C 303 
 TYR   0.014   0.001   TYR E 219 
 PHE   0.020   0.001   PHE F 294 
 TRP   0.028   0.002   TRP F 276 
 HIS   0.010   0.001   HIS D  80 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00300 /  0.13 (13442)
  covalent geometry    : angle       0.59691 /  0.30 (18286)
  hydrogen bonds       : bond        0.03238 /  2.12 (  564)
  hydrogen bonds       : angle       5.15692 /  3.75 ( 1626)

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

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

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  475 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 404
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ARG cc_start: 0.7334 (ptp-170) cc_final: 0.7120 (ptp-170)
REVERT: A  167 LEU cc_start: 0.5794 (OUTLIER) cc_final: 0.5512 (tp)
REVERT: B   22 PHE cc_start: 0.8106 (m-80) cc_final: 0.7744 (m-80)
REVERT: B   98 ASP cc_start: 0.6594 (p0) cc_final: 0.5823 (p0)
REVERT: B  141 ASP cc_start: 0.7481 (t0) cc_final: 0.7249 (t0)
REVERT: B  253 ASP cc_start: 0.7693 (m-30) cc_final: 0.7355 (m-30)
REVERT: C   65 ARG cc_start: 0.8553 (mtp85) cc_final: 0.8192 (mtt-85)
REVERT: C  135 ASN cc_start: 0.8102 (p0) cc_final: 0.7665 (p0)
REVERT: C  141 ASP cc_start: 0.7676 (t0) cc_final: 0.7364 (m-30)
REVERT: C  151 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.6822 (tpp)
REVERT: C  284 ASN cc_start: 0.7981 (t0) cc_final: 0.7567 (t0)
REVERT: D   94 ARG cc_start: 0.8132 (mtp-110) cc_final: 0.7711 (mtp85)
REVERT: D  132 TYR cc_start: 0.7683 (t80) cc_final: 0.7327 (t80)
REVERT: D  254 MET cc_start: 0.7488 (ttm) cc_final: 0.7204 (ttm)
REVERT: D  286 VAL cc_start: 0.8706 (p) cc_final: 0.8471 (m)
REVERT: D  291 ARG cc_start: 0.7672 (mtp180) cc_final: 0.7357 (mtp85)
REVERT: E  147 ARG cc_start: 0.8022 (ttm-80) cc_final: 0.7318 (mtm-85)
REVERT: E  227 ASN cc_start: 0.8242 (m-40) cc_final: 0.7981 (m110)
REVERT: E  254 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.6998 (mpp)
REVERT: E  268 MET cc_start: 0.7856 (tpp) cc_final: 0.7163 (tpp)
REVERT: F  184 THR cc_start: 0.0302 (OUTLIER) cc_final: 0.0036 (m)
REVERT: F  247 LYS cc_start: 0.8613 (mtmt) cc_final: 0.8372 (mtmt)
REVERT: F  259 PHE cc_start: 0.6975 (t80) cc_final: 0.6683 (t80)
REVERT: F  303 ARG cc_start: 0.7270 (ttm110) cc_final: 0.6979 (ttm110)
REVERT: F  309 PHE cc_start: 0.7365 (m-10) cc_final: 0.7009 (m-10)
REVERT: F  314 PHE cc_start: 0.6487 (m-80) cc_final: 0.6154 (m-80)
  outliers start: 71
  outliers final: 56
  residues processed: 445
  average time/residue: 0.1108
  time to fit residues: 69.9181
Evaluate side-chains
  463 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 403
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   29 MET
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   92 CYS
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  208 MET
Chi-restraints excluded: chain B residue   37 ASP
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  170 SER
Chi-restraints excluded: chain B residue  173 ILE
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  222 HIS
Chi-restraints excluded: chain B residue  250 ARG
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  290 PHE
Chi-restraints excluded: chain B residue  296 ASN
Chi-restraints excluded: chain C residue   92 CYS
Chi-restraints excluded: chain C residue   97 LEU
Chi-restraints excluded: chain C residue  105 ASP
Chi-restraints excluded: chain C residue  125 ASP
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  151 MET
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  243 GLU
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  173 ILE
Chi-restraints excluded: chain D residue  186 ASN
Chi-restraints excluded: chain D residue  222 HIS
Chi-restraints excluded: chain D residue  238 ASN
Chi-restraints excluded: chain D residue  295 LEU
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain E residue   46 ASP
Chi-restraints excluded: chain E residue   58 LEU
Chi-restraints excluded: chain E residue   64 ASN
Chi-restraints excluded: chain E residue   77 LYS
Chi-restraints excluded: chain E residue   92 CYS
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain E residue  100 HIS
Chi-restraints excluded: chain E residue  121 THR
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain E residue  173 ILE
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain E residue  217 LEU
Chi-restraints excluded: chain E residue  254 MET
Chi-restraints excluded: chain E residue  264 LEU
Chi-restraints excluded: chain E residue  291 ARG
Chi-restraints excluded: chain E residue  295 LEU
Chi-restraints excluded: chain F residue   13 ASP
Chi-restraints excluded: chain F residue   15 THR
Chi-restraints excluded: chain F residue  166 LEU
Chi-restraints excluded: chain F residue  184 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 140 optimal weight:    4.9990
   chunk 86 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 157 optimal weight:    9.9990
   chunk 118 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 139 optimal weight:    0.9980
   chunk 129 optimal weight:    1.9990
   overall best weight:    1.1182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  80 HIS
E  64 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.163713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.125795 restraints weight = 21734.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.130206 restraints weight = 11582.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.133232 restraints weight = 7600.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.135278 restraints weight = 5708.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.136494 restraints weight = 4719.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7188
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  13442  Z= 0.191
  Angle     :  0.630  11.415  18286  Z= 0.318
  Chirality :  0.045   0.309   2080
  Planarity :  0.005   0.059   2381
  Dihedral  :  4.354  20.745   1822
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 35.61 %
    Favored  : 59.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.28 (0.21), residues: 1632
  helix:  0.43 (0.20), residues: 675
  sheet:  0.56 (0.37), residues: 212
  loop : -0.94 (0.23), residues: 745

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 303 
 TYR   0.016   0.001   TYR E 219 
 PHE   0.027   0.002   PHE F 294 
 TRP   0.022   0.002   TRP F 276 
 HIS   0.015   0.001   HIS D  80 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00432 /  0.19 (13442)
  covalent geometry    : angle       0.62969 /  0.32 (18286)
  hydrogen bonds       : bond        0.03681 /  2.41 (  564)
  hydrogen bonds       : angle       5.20783 /  3.78 ( 1626)

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

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

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  478 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 407
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ARG cc_start: 0.7357 (ptp-170) cc_final: 0.7133 (ptp-170)
REVERT: A  167 LEU cc_start: 0.5938 (OUTLIER) cc_final: 0.5650 (tp)
REVERT: B   22 PHE cc_start: 0.8166 (m-80) cc_final: 0.7787 (m-80)
REVERT: B  141 ASP cc_start: 0.7520 (t0) cc_final: 0.7305 (t0)
REVERT: B  253 ASP cc_start: 0.7742 (m-30) cc_final: 0.7412 (m-30)
REVERT: C   65 ARG cc_start: 0.8550 (mtp85) cc_final: 0.8208 (mtt-85)
REVERT: C   87 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8374 (tpp80)
REVERT: C  135 ASN cc_start: 0.8152 (p0) cc_final: 0.7690 (p0)
REVERT: C  141 ASP cc_start: 0.7743 (t0) cc_final: 0.7377 (m-30)
REVERT: C  151 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.6859 (tpp)
REVERT: C  215 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8309 (p)
REVERT: C  284 ASN cc_start: 0.8019 (t0) cc_final: 0.7628 (t0)
REVERT: C  290 PHE cc_start: 0.7799 (t80) cc_final: 0.7334 (t80)
REVERT: D   30 VAL cc_start: 0.8623 (t) cc_final: 0.8403 (p)
REVERT: D   80 HIS cc_start: 0.7645 (OUTLIER) cc_final: 0.7354 (t70)
REVERT: D   94 ARG cc_start: 0.8173 (mtp-110) cc_final: 0.7664 (mtm110)
REVERT: D  132 TYR cc_start: 0.7745 (t80) cc_final: 0.7400 (t80)
REVERT: D  139 VAL cc_start: 0.8333 (t) cc_final: 0.7987 (m)
REVERT: D  182 PHE cc_start: 0.8026 (m-10) cc_final: 0.7801 (m-10)
REVERT: D  257 GLN cc_start: 0.7752 (tp-100) cc_final: 0.7413 (tp-100)
REVERT: D  286 VAL cc_start: 0.8700 (p) cc_final: 0.8464 (m)
REVERT: D  291 ARG cc_start: 0.7708 (mtp180) cc_final: 0.7401 (mtp85)
REVERT: D  320 GLU cc_start: 0.1550 (OUTLIER) cc_final: 0.1274 (pm20)
REVERT: E  147 ARG cc_start: 0.8059 (ttm-80) cc_final: 0.7351 (mtm-85)
REVERT: E  227 ASN cc_start: 0.8281 (m-40) cc_final: 0.8032 (m110)
REVERT: E  254 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7041 (mpp)
REVERT: E  268 MET cc_start: 0.7927 (tpp) cc_final: 0.7297 (tpp)
REVERT: F  140 PHE cc_start: 0.6594 (m-80) cc_final: 0.6179 (m-80)
REVERT: F  247 LYS cc_start: 0.8698 (mtmt) cc_final: 0.8433 (mtmt)
REVERT: F  259 PHE cc_start: 0.7030 (t80) cc_final: 0.6738 (t80)
REVERT: F  303 ARG cc_start: 0.7299 (ttm110) cc_final: 0.7014 (ttm110)
REVERT: F  309 PHE cc_start: 0.7480 (m-10) cc_final: 0.7107 (m-10)
REVERT: F  314 PHE cc_start: 0.6600 (m-80) cc_final: 0.6277 (m-80)
  outliers start: 71
  outliers final: 58
  residues processed: 444
  average time/residue: 0.1280
  time to fit residues: 79.3345
Evaluate side-chains
  474 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 409
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   92 CYS
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  208 MET
Chi-restraints excluded: chain B residue   37 ASP
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  173 ILE
Chi-restraints excluded: chain B residue  210 ARG
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  222 HIS
Chi-restraints excluded: chain B residue  250 ARG
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  290 PHE
Chi-restraints excluded: chain B residue  296 ASN
Chi-restraints excluded: chain C residue   87 ARG
Chi-restraints excluded: chain C residue   92 CYS
Chi-restraints excluded: chain C residue   97 LEU
Chi-restraints excluded: chain C residue  105 ASP
Chi-restraints excluded: chain C residue  125 ASP
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  151 MET
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  235 HIS
Chi-restraints excluded: chain C residue  243 GLU
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue   92 CYS
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  173 ILE
Chi-restraints excluded: chain D residue  186 ASN
Chi-restraints excluded: chain D residue  222 HIS
Chi-restraints excluded: chain D residue  238 ASN
Chi-restraints excluded: chain D residue  295 LEU
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  320 GLU
Chi-restraints excluded: chain E residue   46 ASP
Chi-restraints excluded: chain E residue   58 LEU
Chi-restraints excluded: chain E residue   64 ASN
Chi-restraints excluded: chain E residue   77 LYS
Chi-restraints excluded: chain E residue   92 CYS
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain E residue  100 HIS
Chi-restraints excluded: chain E residue  121 THR
Chi-restraints excluded: chain E residue  173 ILE
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain E residue  217 LEU
Chi-restraints excluded: chain E residue  244 ILE
Chi-restraints excluded: chain E residue  254 MET
Chi-restraints excluded: chain E residue  264 LEU
Chi-restraints excluded: chain E residue  291 ARG
Chi-restraints excluded: chain E residue  295 LEU
Chi-restraints excluded: chain F residue   13 ASP
Chi-restraints excluded: chain F residue   15 THR
Chi-restraints excluded: chain F residue   28 MET
Chi-restraints excluded: chain F residue  166 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 80 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 93 optimal weight:    4.9990
   chunk 157 optimal weight:    8.9990
   chunk 153 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   chunk 87 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 3 optimal weight:    9.9990
   chunk 85 optimal weight:    0.1980
   chunk 130 optimal weight:    0.9980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  80 HIS
E  64 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.164386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.126866 restraints weight = 21428.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.131315 restraints weight = 11486.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.134253 restraints weight = 7559.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.136014 restraints weight = 5725.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.137500 restraints weight = 4772.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13442  Z= 0.151
  Angle     :  0.623  14.334  18286  Z= 0.310
  Chirality :  0.044   0.320   2080
  Planarity :  0.005   0.059   2381
  Dihedral  :  4.297  21.024   1822
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 35.61 %
    Favored  : 59.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.21), residues: 1632
  helix:  0.50 (0.20), residues: 675
  sheet:  0.54 (0.36), residues: 226
  loop : -0.92 (0.23), residues: 731

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG C 303 
 TYR   0.015   0.001   TYR E 219 
 PHE   0.021   0.001   PHE F 294 
 TRP   0.019   0.002   TRP F 276 
 HIS   0.017   0.001   HIS D  80 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.15 (13442)
  covalent geometry    : angle       0.62350 /  0.31 (18286)
  hydrogen bonds       : bond        0.03362 /  2.21 (  564)
  hydrogen bonds       : angle       5.16096 /  3.75 ( 1626)

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

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

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  475 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 403
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ARG cc_start: 0.7338 (ptp-170) cc_final: 0.7082 (ptp-170)
REVERT: A  167 LEU cc_start: 0.5912 (OUTLIER) cc_final: 0.5628 (tp)
REVERT: B  253 ASP cc_start: 0.7693 (m-30) cc_final: 0.7375 (m-30)
REVERT: C   65 ARG cc_start: 0.8534 (mtp85) cc_final: 0.8188 (mtt-85)
REVERT: C   87 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8333 (tpp80)
REVERT: C  135 ASN cc_start: 0.8120 (p0) cc_final: 0.7686 (p0)
REVERT: C  141 ASP cc_start: 0.7677 (t0) cc_final: 0.7352 (m-30)
REVERT: C  151 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.6815 (tpp)
REVERT: C  215 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8334 (p)
REVERT: C  284 ASN cc_start: 0.8001 (t0) cc_final: 0.7628 (t0)
REVERT: C  290 PHE cc_start: 0.7784 (t80) cc_final: 0.7286 (t80)
REVERT: D   94 ARG cc_start: 0.8146 (mtp-110) cc_final: 0.7645 (mtm110)
REVERT: D  132 TYR cc_start: 0.7691 (t80) cc_final: 0.7333 (t80)
REVERT: D  139 VAL cc_start: 0.8339 (t) cc_final: 0.7957 (m)
REVERT: D  215 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8269 (t)
REVERT: D  253 ASP cc_start: 0.6917 (m-30) cc_final: 0.6554 (m-30)
REVERT: D  286 VAL cc_start: 0.8689 (p) cc_final: 0.8460 (m)
REVERT: D  291 ARG cc_start: 0.7675 (mtp180) cc_final: 0.7356 (mtp85)
REVERT: D  320 GLU cc_start: 0.1529 (OUTLIER) cc_final: 0.1261 (pm20)
REVERT: E   89 ASN cc_start: 0.7989 (t0) cc_final: 0.7661 (t0)
REVERT: E  147 ARG cc_start: 0.8039 (ttm-80) cc_final: 0.7352 (mtm-85)
REVERT: E  227 ASN cc_start: 0.8261 (m-40) cc_final: 0.8001 (m110)
REVERT: E  254 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7033 (mpp)
REVERT: E  268 MET cc_start: 0.7898 (tpp) cc_final: 0.7266 (tpp)
REVERT: F  140 PHE cc_start: 0.6633 (m-80) cc_final: 0.6189 (m-80)
REVERT: F  247 LYS cc_start: 0.8687 (mtmt) cc_final: 0.8404 (mtmt)
REVERT: F  259 PHE cc_start: 0.6971 (t80) cc_final: 0.6685 (t80)
REVERT: F  269 SER cc_start: 0.8431 (m) cc_final: 0.8079 (p)
REVERT: F  271 ARG cc_start: 0.7887 (ttm-80) cc_final: 0.7645 (ttm170)
REVERT: F  303 ARG cc_start: 0.7292 (ttm110) cc_final: 0.6935 (ttm110)
REVERT: F  309 PHE cc_start: 0.7459 (m-10) cc_final: 0.7107 (m-10)
REVERT: F  314 PHE cc_start: 0.6574 (m-80) cc_final: 0.6274 (m-80)
  outliers start: 72
  outliers final: 58
  residues processed: 445
  average time/residue: 0.1234
  time to fit residues: 76.8993
Evaluate side-chains
  465 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 400
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   92 CYS
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  208 MET
Chi-restraints excluded: chain B residue   37 ASP
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  173 ILE
Chi-restraints excluded: chain B residue  210 ARG
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  222 HIS
Chi-restraints excluded: chain B residue  250 ARG
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  290 PHE
Chi-restraints excluded: chain B residue  296 ASN
Chi-restraints excluded: chain C residue   87 ARG
Chi-restraints excluded: chain C residue   92 CYS
Chi-restraints excluded: chain C residue   97 LEU
Chi-restraints excluded: chain C residue  123 PHE
Chi-restraints excluded: chain C residue  125 ASP
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  151 MET
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  235 HIS
Chi-restraints excluded: chain C residue  243 GLU
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  173 ILE
Chi-restraints excluded: chain D residue  186 ASN
Chi-restraints excluded: chain D residue  215 THR
Chi-restraints excluded: chain D residue  222 HIS
Chi-restraints excluded: chain D residue  238 ASN
Chi-restraints excluded: chain D residue  295 LEU
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  320 GLU
Chi-restraints excluded: chain E residue   46 ASP
Chi-restraints excluded: chain E residue   58 LEU
Chi-restraints excluded: chain E residue   64 ASN
Chi-restraints excluded: chain E residue   77 LYS
Chi-restraints excluded: chain E residue   92 CYS
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain E residue  100 HIS
Chi-restraints excluded: chain E residue  121 THR
Chi-restraints excluded: chain E residue  173 ILE
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain E residue  217 LEU
Chi-restraints excluded: chain E residue  254 MET
Chi-restraints excluded: chain E residue  264 LEU
Chi-restraints excluded: chain E residue  269 SER
Chi-restraints excluded: chain E residue  291 ARG
Chi-restraints excluded: chain E residue  295 LEU
Chi-restraints excluded: chain F residue   13 ASP
Chi-restraints excluded: chain F residue   15 THR
Chi-restraints excluded: chain F residue  166 LEU
Chi-restraints excluded: chain F residue  236 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 107 optimal weight:    2.9990
   chunk 127 optimal weight:    0.4980
   chunk 120 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 111 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0270
   chunk 52 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    1.0242

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  80 HIS
E  64 ASN
E 257 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.163714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.125974 restraints weight = 21650.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.130389 restraints weight = 11566.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.133432 restraints weight = 7636.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.135142 restraints weight = 5747.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.136649 restraints weight = 4816.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7179
moved from start:          0.2490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  13442  Z= 0.181
  Angle     :  0.642  11.565  18286  Z= 0.323
  Chirality :  0.045   0.340   2080
  Planarity :  0.005   0.059   2381
  Dihedral  :  4.390  20.504   1822
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 36.39 %
    Favored  : 58.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.21), residues: 1632
  helix:  0.43 (0.20), residues: 675
  sheet:  0.52 (0.36), residues: 226
  loop : -0.95 (0.23), residues: 731

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG C 303 
 TYR   0.020   0.001   TYR E 219 
 PHE   0.022   0.002   PHE F 294 
 TRP   0.018   0.002   TRP F 276 
 HIS   0.013   0.001   HIS D  80 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00411 /  0.18 (13442)
  covalent geometry    : angle       0.64200 /  0.32 (18286)
  hydrogen bonds       : bond        0.03629 /  2.38 (  564)
  hydrogen bonds       : angle       5.21289 /  3.79 ( 1626)

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

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

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  473 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 401
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 LEU cc_start: 0.5993 (OUTLIER) cc_final: 0.5693 (tp)
REVERT: A  210 ARG cc_start: 0.7403 (mmm160) cc_final: 0.7034 (mmm160)
REVERT: B   22 PHE cc_start: 0.8205 (m-80) cc_final: 0.7917 (m-80)
REVERT: B  180 ARG cc_start: 0.8073 (mmt-90) cc_final: 0.7783 (mpt180)
REVERT: B  253 ASP cc_start: 0.7742 (m-30) cc_final: 0.7425 (m-30)
REVERT: C   65 ARG cc_start: 0.8556 (mtp85) cc_final: 0.8203 (mtt-85)
REVERT: C   87 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8309 (tpp80)
REVERT: C  135 ASN cc_start: 0.8139 (p0) cc_final: 0.7676 (p0)
REVERT: C  141 ASP cc_start: 0.7696 (t0) cc_final: 0.7350 (m-30)
REVERT: C  151 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6836 (tpp)
REVERT: C  215 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8339 (p)
REVERT: C  248 MET cc_start: 0.7261 (ttt) cc_final: 0.6676 (ttp)
REVERT: C  284 ASN cc_start: 0.8023 (t0) cc_final: 0.7665 (t0)
REVERT: D   80 HIS cc_start: 0.7654 (OUTLIER) cc_final: 0.7360 (t70)
REVERT: D   94 ARG cc_start: 0.8162 (mtp-110) cc_final: 0.7664 (mtm110)
REVERT: D  132 TYR cc_start: 0.7718 (t80) cc_final: 0.7412 (t80)
REVERT: D  139 VAL cc_start: 0.8344 (t) cc_final: 0.7977 (m)
REVERT: D  253 ASP cc_start: 0.6989 (m-30) cc_final: 0.6640 (m-30)
REVERT: E   37 ASP cc_start: 0.7430 (m-30) cc_final: 0.7223 (m-30)
REVERT: E   89 ASN cc_start: 0.7857 (t0) cc_final: 0.7535 (t0)
REVERT: E  147 ARG cc_start: 0.8060 (ttm-80) cc_final: 0.7375 (mtm-85)
REVERT: E  227 ASN cc_start: 0.8281 (m-40) cc_final: 0.8021 (m110)
REVERT: E  251 VAL cc_start: 0.8875 (m) cc_final: 0.8169 (p)
REVERT: E  254 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7039 (mpp)
REVERT: E  268 MET cc_start: 0.7893 (tpp) cc_final: 0.7354 (tpp)
REVERT: F  140 PHE cc_start: 0.6659 (m-80) cc_final: 0.6183 (m-80)
REVERT: F  247 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8431 (mtmt)
REVERT: F  259 PHE cc_start: 0.7003 (t80) cc_final: 0.6726 (t80)
REVERT: F  271 ARG cc_start: 0.7931 (ttm-80) cc_final: 0.7650 (ttm170)
REVERT: F  303 ARG cc_start: 0.7349 (ttm110) cc_final: 0.7022 (ttm110)
REVERT: F  309 PHE cc_start: 0.7493 (m-10) cc_final: 0.7164 (m-10)
  outliers start: 72
  outliers final: 61
  residues processed: 440
  average time/residue: 0.1229
  time to fit residues: 75.5687
Evaluate side-chains
  466 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 399
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   92 CYS
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  208 MET
Chi-restraints excluded: chain B residue   37 ASP
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  170 SER
Chi-restraints excluded: chain B residue  173 ILE
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  210 ARG
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  222 HIS
Chi-restraints excluded: chain B residue  250 ARG
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  290 PHE
Chi-restraints excluded: chain B residue  296 ASN
Chi-restraints excluded: chain C residue   87 ARG
Chi-restraints excluded: chain C residue   92 CYS
Chi-restraints excluded: chain C residue   97 LEU
Chi-restraints excluded: chain C residue  125 ASP
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  128 LEU
Chi-restraints excluded: chain C residue  151 MET
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  235 HIS
Chi-restraints excluded: chain C residue  243 GLU
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue   92 CYS
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  173 ILE
Chi-restraints excluded: chain D residue  186 ASN
Chi-restraints excluded: chain D residue  222 HIS
Chi-restraints excluded: chain D residue  238 ASN
Chi-restraints excluded: chain D residue  295 LEU
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain E residue   46 ASP
Chi-restraints excluded: chain E residue   58 LEU
Chi-restraints excluded: chain E residue   64 ASN
Chi-restraints excluded: chain E residue   77 LYS
Chi-restraints excluded: chain E residue   92 CYS
Chi-restraints excluded: chain E residue  100 HIS
Chi-restraints excluded: chain E residue  121 THR
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain E residue  173 ILE
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain E residue  217 LEU
Chi-restraints excluded: chain E residue  254 MET
Chi-restraints excluded: chain E residue  264 LEU
Chi-restraints excluded: chain E residue  269 SER
Chi-restraints excluded: chain E residue  291 ARG
Chi-restraints excluded: chain E residue  295 LEU
Chi-restraints excluded: chain F residue   13 ASP
Chi-restraints excluded: chain F residue   15 THR
Chi-restraints excluded: chain F residue  166 LEU
Chi-restraints excluded: chain F residue  236 TYR
Chi-restraints excluded: chain F residue  244 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 121 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 114 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0060
   chunk 24 optimal weight:    0.8980
   chunk 123 optimal weight:    0.5980
   chunk 97 optimal weight:    0.7980
   chunk 75 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 67 optimal weight:    0.8980
   chunk 69 optimal weight:    5.9990
   overall best weight:    0.5796

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  80 HIS
E  64 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.165170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.127700 restraints weight = 21503.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.132190 restraints weight = 11476.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.134948 restraints weight = 7556.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.137067 restraints weight = 5779.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.138215 restraints weight = 4764.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.2545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13442  Z= 0.132
  Angle     :  0.637  13.319  18286  Z= 0.316
  Chirality :  0.044   0.335   2080
  Planarity :  0.005   0.059   2381
  Dihedral  :  4.295  21.230   1822
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 37.09 %
    Favored  : 58.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.21), residues: 1632
  helix:  0.48 (0.20), residues: 676
  sheet:  0.58 (0.36), residues: 228
  loop : -0.90 (0.23), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG C 303 
 TYR   0.018   0.001   TYR E 219 
 PHE   0.019   0.001   PHE F 294 
 TRP   0.026   0.002   TRP F 276 
 HIS   0.007   0.001   HIS D  80 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.13 (13442)
  covalent geometry    : angle       0.63748 /  0.32 (18286)
  hydrogen bonds       : bond        0.03266 /  2.16 (  564)
  hydrogen bonds       : angle       5.12544 /  3.73 ( 1626)

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

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

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  466 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 399
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 LEU cc_start: 0.5967 (OUTLIER) cc_final: 0.5676 (tp)
REVERT: A  210 ARG cc_start: 0.7387 (mmm160) cc_final: 0.6999 (mmm160)
REVERT: B   22 PHE cc_start: 0.8150 (m-80) cc_final: 0.7852 (m-80)
REVERT: B   98 ASP cc_start: 0.6561 (p0) cc_final: 0.5793 (p0)
REVERT: B  155 GLN cc_start: 0.7811 (tt0) cc_final: 0.7104 (tt0)
REVERT: B  253 ASP cc_start: 0.7707 (m-30) cc_final: 0.7379 (m-30)
REVERT: C   65 ARG cc_start: 0.8537 (mtp85) cc_final: 0.8189 (mtt-85)
REVERT: C   87 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8361 (tpp80)
REVERT: C  128 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7366 (mp)
REVERT: C  135 ASN cc_start: 0.8113 (p0) cc_final: 0.7689 (p0)
REVERT: C  141 ASP cc_start: 0.7643 (t0) cc_final: 0.7311 (m-30)
REVERT: C  151 MET cc_start: 0.7319 (OUTLIER) cc_final: 0.6820 (tpp)
REVERT: C  215 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8263 (p)
REVERT: C  248 MET cc_start: 0.7230 (ttt) cc_final: 0.6645 (ttp)
REVERT: C  284 ASN cc_start: 0.7980 (t0) cc_final: 0.7619 (t0)
REVERT: C  290 PHE cc_start: 0.7760 (t80) cc_final: 0.7258 (t80)
REVERT: D   94 ARG cc_start: 0.8140 (mtp-110) cc_final: 0.7693 (mtm110)
REVERT: D  132 TYR cc_start: 0.7646 (t80) cc_final: 0.7336 (t80)
REVERT: D  139 VAL cc_start: 0.8333 (t) cc_final: 0.7961 (m)
REVERT: D  215 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8277 (t)
REVERT: D  253 ASP cc_start: 0.6910 (m-30) cc_final: 0.6549 (m-30)
REVERT: E   89 ASN cc_start: 0.7953 (t0) cc_final: 0.7654 (t0)
REVERT: E  147 ARG cc_start: 0.8031 (ttm-80) cc_final: 0.7364 (mtm-85)
REVERT: E  227 ASN cc_start: 0.8264 (m-40) cc_final: 0.7987 (m110)
REVERT: E  251 VAL cc_start: 0.8851 (m) cc_final: 0.8160 (p)
REVERT: E  254 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7036 (mpp)
REVERT: E  268 MET cc_start: 0.7854 (tpp) cc_final: 0.7306 (tpp)
REVERT: F  140 PHE cc_start: 0.6659 (m-80) cc_final: 0.6219 (m-80)
REVERT: F  247 LYS cc_start: 0.8680 (mtmt) cc_final: 0.8403 (mtmt)
REVERT: F  269 SER cc_start: 0.8336 (m) cc_final: 0.8021 (p)
REVERT: F  271 ARG cc_start: 0.7913 (ttm-80) cc_final: 0.7690 (ttm170)
REVERT: F  303 ARG cc_start: 0.7399 (ttm110) cc_final: 0.7035 (ttm110)
REVERT: F  309 PHE cc_start: 0.7480 (m-10) cc_final: 0.7135 (m-10)
  outliers start: 67
  outliers final: 57
  residues processed: 436
  average time/residue: 0.1244
  time to fit residues: 75.6579
Evaluate side-chains
  460 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 396
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   92 CYS
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  208 MET
Chi-restraints excluded: chain B residue   13 ASP
Chi-restraints excluded: chain B residue   37 ASP
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  173 ILE
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  210 ARG
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  222 HIS
Chi-restraints excluded: chain B residue  250 ARG
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  290 PHE
Chi-restraints excluded: chain B residue  296 ASN
Chi-restraints excluded: chain C residue   87 ARG
Chi-restraints excluded: chain C residue   92 CYS
Chi-restraints excluded: chain C residue   97 LEU
Chi-restraints excluded: chain C residue  125 ASP
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  128 LEU
Chi-restraints excluded: chain C residue  151 MET
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  243 GLU
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue   92 CYS
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  173 ILE
Chi-restraints excluded: chain D residue  186 ASN
Chi-restraints excluded: chain D residue  215 THR
Chi-restraints excluded: chain D residue  222 HIS
Chi-restraints excluded: chain D residue  238 ASN
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain E residue   46 ASP
Chi-restraints excluded: chain E residue   58 LEU
Chi-restraints excluded: chain E residue   64 ASN
Chi-restraints excluded: chain E residue   77 LYS
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain E residue  100 HIS
Chi-restraints excluded: chain E residue  121 THR
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain E residue  173 ILE
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain E residue  217 LEU
Chi-restraints excluded: chain E residue  254 MET
Chi-restraints excluded: chain E residue  264 LEU
Chi-restraints excluded: chain E residue  269 SER
Chi-restraints excluded: chain E residue  291 ARG
Chi-restraints excluded: chain E residue  295 LEU
Chi-restraints excluded: chain F residue   13 ASP
Chi-restraints excluded: chain F residue  166 LEU
Chi-restraints excluded: chain F residue  236 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 89 optimal weight:    0.7980
   chunk 98 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 25 optimal weight:    3.9990
   chunk 150 optimal weight:    2.9990
   chunk 108 optimal weight:    0.8980
   chunk 93 optimal weight:    0.0010
   chunk 43 optimal weight:    4.9990
   chunk 119 optimal weight:    0.7980
   chunk 158 optimal weight:    2.9990
   chunk 117 optimal weight:    6.9990
   overall best weight:    0.6186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  80 HIS
E  64 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.165073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.128171 restraints weight = 21362.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.132530 restraints weight = 11358.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.135562 restraints weight = 7469.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.137280 restraints weight = 5619.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.138560 restraints weight = 4685.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7144
moved from start:          0.2646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13442  Z= 0.135
  Angle     :  0.638  12.011  18286  Z= 0.317
  Chirality :  0.044   0.334   2080
  Planarity :  0.005   0.089   2381
  Dihedral  :  4.270  21.296   1822
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 36.60 %
    Favored  : 58.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.21), residues: 1632
  helix:  0.50 (0.20), residues: 676
  sheet:  0.55 (0.35), residues: 228
  loop : -0.89 (0.24), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG E  87 
 TYR   0.024   0.001   TYR F 310 
 PHE   0.019   0.001   PHE F 294 
 TRP   0.022   0.002   TRP F 276 
 HIS   0.012   0.001   HIS D  80 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.14 (13442)
  covalent geometry    : angle       0.63753 /  0.32 (18286)
  hydrogen bonds       : bond        0.03281 /  2.17 (  564)
  hydrogen bonds       : angle       5.09990 /  3.71 ( 1626)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2546.58 seconds
wall clock time: 44 minutes 35.70 seconds (2675.70 seconds total)