Starting phenix.real_space_refine
on Tue Jul 29 21:31:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7o16_12691/07_2025/7o16_12691.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7o16_12691/07_2025/7o16_12691.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7o16_12691/07_2025/7o16_12691.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7o16_12691/07_2025/7o16_12691.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7o16_12691/07_2025/7o16_12691.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7o16_12691/07_2025/7o16_12691.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
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: 5
    Type Number    sf(0)   Gaussians
     Mg      1      5.21       5
     S      37      5.16       5
     C    7466      2.51       5
     N    2038      2.21       5
     O    2109      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11651
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 402, 3140
          Classifications: {'peptide': 402}
          Link IDs: {'PTRANS': 16, 'TRANS': 385}
    Chain: "B"
      Number of atoms: 2303
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2303
          Classifications: {'peptide': 299}
          Link IDs: {'PTRANS': 12, 'TRANS': 286}
    Chain: "C"
      Number of atoms: 2295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 298, 2295
          Classifications: {'peptide': 298}
          Link IDs: {'PTRANS': 12, 'TRANS': 285}
    Chain: "D"
      Number of atoms: 2015
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 2015
          Classifications: {'peptide': 267}
          Link IDs: {'PTRANS': 8, 'TRANS': 258}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1896
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 248, 1896
          Classifications: {'peptide': 248}
          Link IDs: {'PTRANS': 8, 'TRANS': 239}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 7.63, per 1000 atoms: 0.65
  Number of scatterers: 11651
  At special positions: 0
  Unit cell: (73.872, 92.016, 190.512, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      37     16.00
     Mg      1     11.99
     O    2109      8.00
     N    2038      7.00
     C    7466      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: 2.45
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2722

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 11 sheets defined
      47.3% alpha, 12.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 30 through 34
    Processing helix  chain 'A' and resid 375 through 383
      removed outlier: 3.588A  pdb=" N   LEU A 380 " --> pdb=" O   VAL A 376 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   TRP A 381 " --> pdb=" O   ASP A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 388
    Processing helix  chain 'A' and resid 392 through 405
      removed outlier: 3.629A  pdb=" N   GLN A 402 " --> pdb=" O   LEU A 398 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ARG A 403 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 50
      removed outlier: 3.767A  pdb=" N   ILE B  49 " --> pdb=" O   SER B  45 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   LEU B  50 " --> pdb=" O   MET B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 74
    Processing helix  chain 'B' and resid 90 through 102
      removed outlier: 3.621A  pdb=" N   LEU B  95 " --> pdb=" O   GLY B  91 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ARG B 100 " --> pdb=" O   ARG B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 107
      No H-bonds generated for 'chain 'B' and resid 105 through 107'
    Processing helix  chain 'B' and resid 108 through 116
    Processing helix  chain 'B' and resid 130 through 143
      removed outlier: 3.800A  pdb=" N   ALA B 142 " --> pdb=" O   GLY B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 178
      removed outlier: 3.610A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 172 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ARG B 177 " --> pdb=" O   ARG B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 192
      removed outlier: 4.111A  pdb=" N   VAL B 191 " --> pdb=" O   VAL B 187 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLU B 192 " --> pdb=" O   LEU B 188 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 187 through 192'
    Processing helix  chain 'B' and resid 211 through 219
    Processing helix  chain 'B' and resid 232 through 244
      removed outlier: 4.229A  pdb=" N   GLN B 238 " --> pdb=" O   ASP B 234 " (cutoff:3.500A)
      removed outlier: 4.768A  pdb=" N   ARG B 239 " --> pdb=" O   SER B 235 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   TRP B 240 " --> pdb=" O   TRP B 236 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   THR B 241 " --> pdb=" O   LEU B 237 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ASP B 242 " --> pdb=" O   GLN B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 275
      removed outlier: 3.518A  pdb=" N   LEU B 268 " --> pdb=" O   LYS B 264 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ARG B 269 " --> pdb=" O   LEU B 265 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLN B 270 " --> pdb=" O   VAL B 266 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   GLU B 274 " --> pdb=" O   GLN B 270 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   GLY B 275 " --> pdb=" O   LEU B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 298
      removed outlier: 3.523A  pdb=" N   ALA B 298 " --> pdb=" O   TYR B 294 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 41 through 50
      removed outlier: 3.826A  pdb=" N   SER C  45 " --> pdb=" O   GLY C  41 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ILE C  49 " --> pdb=" O   SER C  45 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU C  50 " --> pdb=" O   MET C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 69 through 74
    Processing helix  chain 'C' and resid 90 through 102
      removed outlier: 3.530A  pdb=" N   THR C  94 " --> pdb=" O   SER C  90 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 105 through 109
      removed outlier: 3.803A  pdb=" N   VAL C 109 " --> pdb=" O   LEU C 106 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 125 through 129
    Processing helix  chain 'C' and resid 130 through 141
    Processing helix  chain 'C' and resid 160 through 177
      removed outlier: 3.694A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 172 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 190 through 194
      removed outlier: 3.647A  pdb=" N   ALA C 193 " --> pdb=" O   GLY C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 212 through 218
    Processing helix  chain 'C' and resid 234 through 238
    Processing helix  chain 'C' and resid 240 through 244
      removed outlier: 3.588A  pdb=" N   ALA C 243 " --> pdb=" O   TRP C 240 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 263 through 274
      removed outlier: 3.957A  pdb=" N   LEU C 268 " --> pdb=" O   LYS C 264 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   GLU C 274 " --> pdb=" O   GLN C 270 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 286 through 299
      removed outlier: 3.859A  pdb=" N   GLU C 296 " --> pdb=" O   ARG C 292 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 15
      removed outlier: 3.533A  pdb=" N   ILE D   7 " --> pdb=" O   GLN D   3 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   LYS D  10 " --> pdb=" O   ASN D   6 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   GLU D  11 " --> pdb=" O   ILE D   7 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 18 through 42
      removed outlier: 3.608A  pdb=" N   ILE D  24 " --> pdb=" O   TRP D  20 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   PHE D  28 " --> pdb=" O   ILE D  24 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLY D  34 " --> pdb=" O   VAL D  30 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ALA D  36 " --> pdb=" O   ALA D  32 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 51 through 75
      removed outlier: 3.649A  pdb=" N   ALA D  56 " --> pdb=" O   PRO D  52 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   LEU D  58 " --> pdb=" O   THR D  54 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   SER D  60 " --> pdb=" O   ALA D  56 " (cutoff:3.500A)
      Proline residue:  D  67  - end of helix
      removed outlier: 3.582A  pdb=" N   TYR D  75 " --> pdb=" O   LEU D  71 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 78 through 83
    Processing helix  chain 'D' and resid 85 through 91
      removed outlier: 3.634A  pdb=" N   LEU D  89 " --> pdb=" O   GLY D  85 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 98 through 129
      removed outlier: 4.024A  pdb=" N   LYS D 104 " --> pdb=" O   ILE D 100 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ILE D 111 " --> pdb=" O   GLY D 107 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU D 117 " --> pdb=" O   ALA D 113 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLY D 119 " --> pdb=" O   ALA D 115 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE D 127 " --> pdb=" O   ALA D 123 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU D 129 " --> pdb=" O   LEU D 125 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 135 through 167
      removed outlier: 3.623A  pdb=" N   SER D 149 " --> pdb=" O   ARG D 145 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   THR D 151 " --> pdb=" O   MET D 147 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   LEU D 152 " --> pdb=" O   ILE D 148 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   VAL D 163 " --> pdb=" O   ALA D 159 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 170 through 188
      removed outlier: 3.748A  pdb=" N   GLY D 176 " --> pdb=" O   SER D 172 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   VAL D 186 " --> pdb=" O   TRP D 182 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   VAL D 188 " --> pdb=" O   LEU D 184 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 188 through 200
      removed outlier: 3.505A  pdb=" N   LEU D 194 " --> pdb=" O   ASP D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 214
    Processing helix  chain 'D' and resid 216 through 226
      removed outlier: 3.577A  pdb=" N   ASN D 225 " --> pdb=" O   TYR D 221 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 232 through 237
      removed outlier: 4.001A  pdb=" N   MET D 236 " --> pdb=" O   SER D 232 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 238 through 244
      removed outlier: 3.668A  pdb=" N   ALA D 243 " --> pdb=" O   SER D 240 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 248 through 272
      removed outlier: 3.724A  pdb=" N   LEU D 252 " --> pdb=" O   PRO D 248 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   LEU D 256 " --> pdb=" O   LEU D 252 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   SER D 263 " --> pdb=" O   TRP D 259 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ALA D 267 " --> pdb=" O   SER D 263 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 3 through 7
      removed outlier: 3.516A  pdb=" N   ILE E   7 " --> pdb=" O   GLN E   3 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 3 through 7'
    Processing helix  chain 'E' and resid 7 through 16
      removed outlier: 3.541A  pdb=" N   GLU E  11 " --> pdb=" O   ILE E   7 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 18 through 41
      removed outlier: 3.564A  pdb=" N   ILE E  24 " --> pdb=" O   TRP E  20 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ALA E  36 " --> pdb=" O   ALA E  32 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LEU E  38 " --> pdb=" O   GLY E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 52 through 75
      removed outlier: 3.792A  pdb=" N   SER E  57 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   MET E  66 " --> pdb=" O   ALA E  62 " (cutoff:3.500A)
      Proline residue:  E  67  - end of helix
      removed outlier: 3.550A  pdb=" N   TYR E  75 " --> pdb=" O   LEU E  71 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 78 through 84
    Processing helix  chain 'E' and resid 85 through 91
    Processing helix  chain 'E' and resid 96 through 120
      removed outlier: 3.509A  pdb=" N   ILE E 100 " --> pdb=" O   GLY E  96 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LEU E 101 " --> pdb=" O   ARG E  97 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE E 111 " --> pdb=" O   GLY E 107 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   LEU E 112 " --> pdb=" O   HIS E 108 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   LEU E 117 " --> pdb=" O   ALA E 113 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 124 through 129
    Processing helix  chain 'E' and resid 135 through 143
      removed outlier: 3.730A  pdb=" N   LEU E 139 " --> pdb=" O   GLU E 135 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   TRP E 141 " --> pdb=" O   GLY E 137 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 143 through 168
      removed outlier: 3.593A  pdb=" N   VAL E 168 " --> pdb=" O   LEU E 164 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 170 through 188
      removed outlier: 3.527A  pdb=" N   GLY E 176 " --> pdb=" O   SER E 172 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLY E 180 " --> pdb=" O   GLY E 176 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   VAL E 186 " --> pdb=" O   TRP E 182 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   VAL E 188 " --> pdb=" O   LEU E 184 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 190 through 199
    Processing helix  chain 'E' and resid 208 through 213
    Processing helix  chain 'E' and resid 216 through 224
      removed outlier: 3.556A  pdb=" N   ILE E 224 " --> pdb=" O   ILE E 220 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 248 through 272
      removed outlier: 3.891A  pdb=" N   LEU E 252 " --> pdb=" O   PRO E 248 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   SER E 263 " --> pdb=" O   TRP E 259 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 47
      removed outlier: 6.046A  pdb=" N   TRP A  45 " --> pdb=" O   ARG A  65 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58
      removed outlier: 6.468A  pdb=" N   PHE A  56 " --> pdb=" O   LEU A  82 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   GLY A 131 " --> pdb=" O   SER A 107 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ASP A 135 " --> pdb=" O   ILE A 111 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   HIS A 163 " --> pdb=" O   PHE A 130 " (cutoff:3.500A)
      removed outlier: 6.024A  pdb=" N   VAL A 132 " --> pdb=" O   HIS A 163 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   PHE A 165 " --> pdb=" O   VAL A 132 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   VAL A 134 " --> pdb=" O   PHE A 165 " (cutoff:3.500A)
      removed outlier: 5.923A  pdb=" N   ILE A 162 " --> pdb=" O   TYR A 185 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   ASP A 187 " --> pdb=" O   ILE A 162 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   LEU A 164 " --> pdb=" O   ASP A 187 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   ILE A 184 " --> pdb=" O   HIS A 207 " (cutoff:3.500A)
      removed outlier: 7.538A  pdb=" N   MET A 209 " --> pdb=" O   ILE A 184 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   ILE A 186 " --> pdb=" O   MET A 209 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   TYR A 204 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
      removed outlier: 7.341A  pdb=" N   ALA A 229 " --> pdb=" O   TYR A 204 " (cutoff:3.500A)
      removed outlier: 6.061A  pdb=" N   VAL A 206 " --> pdb=" O   ALA A 229 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   MET A 231 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 5.747A  pdb=" N   TYR A 208 " --> pdb=" O   MET A 231 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   THR A 226 " --> pdb=" O   GLY A 250 " (cutoff:3.500A)
      removed outlier: 7.477A  pdb=" N   LEU A 252 " --> pdb=" O   THR A 226 " (cutoff:3.500A)
      removed outlier: 6.042A  pdb=" N   TYR A 228 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      removed outlier: 7.048A  pdb=" N   ASN A 254 " --> pdb=" O   TYR A 228 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   LEU A 230 " --> pdb=" O   ASN A 254 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   LEU A 288 " --> pdb=" O   GLY A 250 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   LEU A 252 " --> pdb=" O   LEU A 288 " (cutoff:3.500A)
      removed outlier: 7.248A  pdb=" N   ILE A 290 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      removed outlier: 7.221A  pdb=" N   ASN A 254 " --> pdb=" O   ILE A 290 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   LYS A 286 " --> pdb=" O   GLY A 309 " (cutoff:3.500A)
      removed outlier: 7.158A  pdb=" N   HIS A 311 " --> pdb=" O   LYS A 286 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   LEU A 288 " --> pdb=" O   HIS A 311 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   GLN A 332 " --> pdb=" O   LEU A 308 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 73
      removed outlier: 6.062A  pdb=" N   THR A  94 " --> pdb=" O   ILE A  72 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   ILE A 147 " --> pdb=" O   ARG A 178 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   VAL A 177 " --> pdb=" O   GLU A 200 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   ILE A 199 " --> pdb=" O   ARG A 222 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   SER A 243 " --> pdb=" O   SER A 267 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   VAL A 266 " --> pdb=" O   GLU A 304 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91
      removed outlier: 6.355A  pdb=" N   VAL A  90 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   VAL A 142 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 217
    Processing sheet with id=AA6, first strand: chain 'B' and resid 17 through 26
      removed outlier: 6.195A  pdb=" N   VAL B  18 " --> pdb=" O   ARG B  12 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   ARG B  12 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   HIS B  20 " --> pdb=" O   SER B  10 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   SER B  10 " --> pdb=" O   HIS B  20 " (cutoff:3.500A)
      removed outlier: 5.801A  pdb=" N   LEU B  22 " --> pdb=" O   GLY B   8 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLY B   8 " --> pdb=" O   LEU B  22 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   VAL B   4 " --> pdb=" O   LEU B  26 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLN B  59 " --> pdb=" O   GLN B   7 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79
      removed outlier: 7.589A  pdb=" N   GLY B  77 " --> pdb=" O   LEU B 151 " (cutoff:3.500A)
      removed outlier: 7.904A  pdb=" N   ASP B 153 " --> pdb=" O   GLY B  77 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   LEU B  79 " --> pdb=" O   ASP B 153 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   LEU B 150 " --> pdb=" O   ILE B 182 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   CYS B 184 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   LEU B 152 " --> pdb=" O   CYS B 184 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   LEU B  32 " --> pdb=" O   LEU B 183 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   GLY B  33 " --> pdb=" O   ALA B 199 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 246 through 248
      removed outlier: 4.240A  pdb=" N   SER B 246 " --> pdb=" O   VAL B 258 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 4 through 7
      removed outlier: 3.549A  pdb=" N   GLN C  59 " --> pdb=" O   GLN C   7 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79
      removed outlier: 6.523A  pdb=" N   GLY C  77 " --> pdb=" O   LEU C 151 " (cutoff:3.500A)
      removed outlier: 7.420A  pdb=" N   ASP C 153 " --> pdb=" O   GLY C  77 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   LEU C  79 " --> pdb=" O   ASP C 153 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   LEU C  32 " --> pdb=" O   LEU C 183 " (cutoff:3.500A)
      removed outlier: 6.141A  pdb=" N   VAL C  31 " --> pdb=" O   ARG C 197 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   ALA C 199 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   GLY C  33 " --> pdb=" O   ALA C 199 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   LEU C 201 " --> pdb=" O   GLY C  33 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   ALA C 198 " --> pdb=" O   VAL C 209 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   VAL C 209 " --> pdb=" O   ALA C 198 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   ILE C 200 " --> pdb=" O   GLN C 207 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 246 through 248
      removed outlier: 3.765A  pdb=" N   ARG C 248 " --> pdb=" O   GLU C 256 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   ILE C 255 " --> pdb=" O   ALA C 227 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ILE C 225 " --> pdb=" O   VAL C 257 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ARG C 226 " --> pdb=" O   GLU C 281 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   SER C 228 " --> pdb=" O   ASP C 279 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ASP C 279 " --> pdb=" O   SER C 228 " (cutoff:3.500A)

    462 hydrogen bonds defined for protein.
    1311 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: 3.38

  Time building geometry restraints manager: 3.00 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: 3640
        1.34 -     1.46: 2105
        1.46 -     1.58: 6059
        1.58 -     1.70: 3
        1.70 -     1.82: 64
  Bond restraints: 11871
  Sorted by residual:
  bond pdb=" CA  ILE E  51 "
       pdb=" C   ILE E  51 "
    ideal  model  delta    sigma   weight residual
    1.525  1.594 -0.069 2.10e-02 2.27e+03 1.07e+01
  bond pdb=" CB  ASN B 261 "
       pdb=" CG  ASN B 261 "
    ideal  model  delta    sigma   weight residual
    1.516  1.587 -0.071 2.50e-02 1.60e+03 8.00e+00
  bond pdb=" CA  ARG C 224 "
       pdb=" CB  ARG C 224 "
    ideal  model  delta    sigma   weight residual
    1.526  1.478  0.048 1.76e-02 3.23e+03 7.39e+00
  bond pdb=" CB  PHE B  35 "
       pdb=" CG  PHE B  35 "
    ideal  model  delta    sigma   weight residual
    1.502  1.447  0.055 2.30e-02 1.89e+03 5.81e+00
  bond pdb=" CA  ASN C 261 "
       pdb=" CB  ASN C 261 "
    ideal  model  delta    sigma   weight residual
    1.529  1.565 -0.036 1.58e-02 4.01e+03 5.27e+00
  ... (remaining 11866 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.69: 15805
        3.69 -     7.38: 271
        7.38 -    11.07: 35
       11.07 -    14.76: 3
       14.76 -    18.45: 2
  Bond angle restraints: 16116
  Sorted by residual:
  angle pdb=" CA  GLU A 213 "
        pdb=" CB  GLU A 213 "
        pdb=" CG  GLU A 213 "
      ideal   model   delta    sigma   weight residual
     114.10  124.99  -10.89 2.00e+00 2.50e-01 2.97e+01
  angle pdb=" N   GLU B 252 "
        pdb=" CA  GLU B 252 "
        pdb=" C   GLU B 252 "
      ideal   model   delta    sigma   weight residual
     108.32   99.39    8.93 1.64e+00 3.72e-01 2.97e+01
  angle pdb=" C   VAL B 260 "
        pdb=" N   ASN B 261 "
        pdb=" CA  ASN B 261 "
      ideal   model   delta    sigma   weight residual
     122.08  129.96   -7.88 1.47e+00 4.63e-01 2.87e+01
  angle pdb=" CA  LEU A 356 "
        pdb=" CB  LEU A 356 "
        pdb=" CG  LEU A 356 "
      ideal   model   delta    sigma   weight residual
     116.30  134.75  -18.45 3.50e+00 8.16e-02 2.78e+01
  angle pdb=" C   GLN A 247 "
        pdb=" N   ASN A 248 "
        pdb=" CA  ASN A 248 "
      ideal   model   delta    sigma   weight residual
     121.54  131.45   -9.91 1.91e+00 2.74e-01 2.69e+01
  ... (remaining 16111 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.12: 6283
       18.12 -    36.24: 587
       36.24 -    54.36: 130
       54.36 -    72.48: 19
       72.48 -    90.61: 2
  Dihedral angle restraints: 7021
    sinusoidal: 2752
      harmonic: 4269
  Sorted by residual:
  dihedral pdb=" CA  LEU B 250 "
           pdb=" C   LEU B 250 "
           pdb=" N   SER B 251 "
           pdb=" CA  SER B 251 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   89.39   90.61     0      5.00e+00 4.00e-02 3.28e+02
  dihedral pdb=" CA  LEU D  73 "
           pdb=" C   LEU D  73 "
           pdb=" N   ALA D  74 "
           pdb=" CA  ALA D  74 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.16  -22.84     0      5.00e+00 4.00e-02 2.09e+01
  dihedral pdb=" CA  PRO B 277 "
           pdb=" C   PRO B 277 "
           pdb=" N   GLU B 278 "
           pdb=" CA  GLU B 278 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.52  -22.48     0      5.00e+00 4.00e-02 2.02e+01
  ... (remaining 7018 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.099: 1639
       0.099 -    0.198: 190
       0.198 -    0.297: 26
       0.297 -    0.396: 3
       0.396 -    0.495: 3
  Chirality restraints: 1861
  Sorted by residual:
  chirality pdb=" CB  VAL A 413 "
            pdb=" CA  VAL A 413 "
            pdb=" CG1 VAL A 413 "
            pdb=" CG2 VAL A 413 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.13   -0.49 2.00e-01 2.50e+01 6.12e+00
  chirality pdb=" CB  VAL A 109 "
            pdb=" CA  VAL A 109 "
            pdb=" CG1 VAL A 109 "
            pdb=" CG2 VAL A 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.16   -0.47 2.00e-01 2.50e+01 5.54e+00
  chirality pdb=" CB  ILE C 255 "
            pdb=" CA  ILE C 255 "
            pdb=" CG1 ILE C 255 "
            pdb=" CG2 ILE C 255 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.19    0.45 2.00e-01 2.50e+01 5.15e+00
  ... (remaining 1858 not shown)

  Planarity restraints: 2063
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B  81 "   -0.018 2.00e-02 2.50e+03   3.79e-02 1.44e+01
        pdb=" C   GLU B  81 "    0.066 2.00e-02 2.50e+03
        pdb=" O   GLU B  81 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   ASN B  82 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 345 "   -0.017 2.00e-02 2.50e+03   3.42e-02 1.17e+01
        pdb=" C   VAL A 345 "    0.059 2.00e-02 2.50e+03
        pdb=" O   VAL A 345 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   ASP A 346 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 376 "    0.016 2.00e-02 2.50e+03   3.26e-02 1.06e+01
        pdb=" C   VAL A 376 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   VAL A 376 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ASP A 377 "    0.019 2.00e-02 2.50e+03
  ... (remaining 2060 not shown)

  Histogram of nonbonded interaction distances:
        1.84 -     2.45: 42
        2.45 -     3.06: 6295
        3.06 -     3.68: 18202
        3.68 -     4.29: 26404
        4.29 -     4.90: 43556
  Nonbonded interactions: 94499
  Sorted by model distance:
  nonbonded pdb="MG    MG A 501 "
            pdb=" O   HOH A 601 "
     model   vdw
     1.840 2.170
  nonbonded pdb=" OD1 ASP A 359 "
            pdb="MG    MG A 501 "
     model   vdw
     1.987 2.170
  nonbonded pdb=" OD1 ASP A 363 "
            pdb="MG    MG A 501 "
     model   vdw
     2.134 2.170
  nonbonded pdb=" OD1 ASN A 361 "
            pdb="MG    MG A 501 "
     model   vdw
     2.200 2.170
  nonbonded pdb=" O   SER A 293 "
            pdb=" OG  SER A 316 "
     model   vdw
     2.331 3.040
  ... (remaining 94494 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 2 through 299)
  selection = chain 'C'
}
ncs_group {
  reference = (chain 'D' and (resid 2 through 42 or resid 51 through 227 or resid 245 through  \ 
274))
  selection = chain 'E'
}

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:             0.750
  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:          0.450
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     28.740
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
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      :  0.008   0.078  11871  Z= 0.342
  Angle     :  1.204  18.446  16116  Z= 0.643
  Chirality :  0.070   0.495   1861
  Planarity :  0.008   0.075   2063
  Dihedral  : 14.533  90.606   4299
  Min Nonbonded Distance : 1.840

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  8.50 %
    Favored  : 90.44 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.77 (0.15), residues: 1498
  helix: -4.62 (0.07), residues: 652
  sheet: -3.35 (0.31), residues: 180
  loop : -2.94 (0.20), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP E 211 
 HIS   0.013   0.002   HIS C  37 
 PHE   0.023   0.003   PHE D 189 
 TYR   0.019   0.003   TYR C  13 
 ARG   0.010   0.001   ARG A 203 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.30303 (  462)
  hydrogen bonds       : angle      10.45541 ( 1311)
  covalent geometry    : bond        0.00751 (11871)
  covalent geometry    : angle       1.20434 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 1.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  209 MET cc_start: 0.9305 (mmm) cc_final: 0.9091 (mmm)
REVERT: A  231 MET cc_start: 0.8925 (mtt) cc_final: 0.8111 (mtp)
REVERT: A  279 MET cc_start: 0.5504 (tpt) cc_final: 0.4978 (ptp)
REVERT: A  422 LEU cc_start: 0.8944 (mt) cc_final: 0.8573 (tp)
REVERT: B   86 TYR cc_start: 0.9008 (m-80) cc_final: 0.8785 (m-80)
REVERT: B  283 HIS cc_start: 0.9115 (m90) cc_final: 0.8665 (m90)
REVERT: C  184 CYS cc_start: 0.8306 (m) cc_final: 0.5649 (m)
REVERT: D   81 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8532 (mt-10)
REVERT: D  219 ASP cc_start: 0.8399 (m-30) cc_final: 0.8167 (m-30)
REVERT: D  222 ARG cc_start: 0.8960 (mtt180) cc_final: 0.8751 (mtm-85)
REVERT: E   66 MET cc_start: 0.9342 (mmm) cc_final: 0.8942 (mmp)
REVERT: E  266 LEU cc_start: 0.9489 (tp) cc_final: 0.9246 (tp)
  outliers start: 13
  outliers final: 5
  residues processed: 115
  average time/residue: 0.2660
  time to fit residues: 43.1182
Evaluate side-chains
  70 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 1.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain C residue  258 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 124 optimal weight:    0.7980
   chunk 112 optimal weight:    4.9990
   chunk 62 optimal weight:    0.7980
   chunk 38 optimal weight:    5.9990
   chunk 75 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 116 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 70 optimal weight:    7.9990
   chunk 86 optimal weight:    7.9990
   chunk 134 optimal weight:    7.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A  53 GLN
A  77 GLN
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 141 GLN
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 160 ASN
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 176 HIS
A 190 ASN
A 212 ASN
A 241 ASN
A 301 ASN
A 324 ASN
A 341 GLN
B   2 ASN
B  11 GLN
B  20 HIS
B  82 ASN
** B  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN
C 115 GLN
C 194 HIS
C 245 HIS
D 225 ASN
E 108 HIS
E 225 ASN

Total number of N/Q/H flips: 22

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.049069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.038674 restraints weight = 72530.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.039843 restraints weight = 40240.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.040647 restraints weight = 26583.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.2029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11871  Z= 0.132
  Angle     :  0.634   9.175  16116  Z= 0.327
  Chirality :  0.042   0.163   1861
  Planarity :  0.005   0.043   2063
  Dihedral  :  5.459  50.201   1647
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.01 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 12.66 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.71 (0.18), residues: 1498
  helix: -2.04 (0.16), residues: 670
  sheet: -2.89 (0.33), residues: 187
  loop : -2.66 (0.22), residues: 641

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 240 
 HIS   0.010   0.001   HIS B 194 
 PHE   0.011   0.001   PHE D 157 
 TYR   0.011   0.001   TYR B 168 
 ARG   0.006   0.000   ARG B 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04041 (  462)
  hydrogen bonds       : angle       4.95274 ( 1311)
  covalent geometry    : bond        0.00283 (11871)
  covalent geometry    : angle       0.63351 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 1.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  231 MET cc_start: 0.8707 (mtt) cc_final: 0.8040 (mtp)
REVERT: A  279 MET cc_start: 0.5732 (tpt) cc_final: 0.5030 (ptp)
REVERT: A  334 LYS cc_start: 0.9258 (tttt) cc_final: 0.9021 (tttp)
REVERT: A  390 MET cc_start: 0.8719 (ptt) cc_final: 0.8352 (ptt)
REVERT: B   16 MET cc_start: 0.8114 (pmm) cc_final: 0.7723 (pmm)
REVERT: B   46 MET cc_start: 0.8664 (mmm) cc_final: 0.8462 (tpt)
REVERT: B  283 HIS cc_start: 0.9087 (m90) cc_final: 0.8670 (m90)
REVERT: C   47 LYS cc_start: 0.9421 (mttt) cc_final: 0.9215 (mtpp)
REVERT: D  138 MET cc_start: 0.8029 (tmm) cc_final: 0.7437 (tmm)
REVERT: D  147 MET cc_start: 0.8527 (mmm) cc_final: 0.8154 (mmt)
REVERT: D  219 ASP cc_start: 0.8380 (m-30) cc_final: 0.8142 (m-30)
REVERT: D  222 ARG cc_start: 0.9121 (mtt180) cc_final: 0.8918 (mtt180)
REVERT: E   10 LYS cc_start: 0.9413 (ttpt) cc_final: 0.9159 (ttpp)
REVERT: E   11 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8636 (mm-30)
REVERT: E   66 MET cc_start: 0.9508 (mmm) cc_final: 0.9293 (mmp)
REVERT: E  187 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.8964 (pp)
  outliers start: 13
  outliers final: 4
  residues processed: 87
  average time/residue: 0.2712
  time to fit residues: 34.8642
Evaluate side-chains
  65 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 1.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain B residue   82 ASN
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain E residue  187 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 109 optimal weight:    7.9990
   chunk 132 optimal weight:    6.9990
   chunk 55 optimal weight:    9.9990
   chunk 77 optimal weight:    0.0040
   chunk 34 optimal weight:    6.9990
   chunk 64 optimal weight:    7.9990
   chunk 72 optimal weight:    0.9990
   chunk 102 optimal weight:    8.9990
   chunk 84 optimal weight:    9.9990
   chunk 98 optimal weight:    2.9990
   chunk 94 optimal weight:   20.0000
   overall best weight:    3.6000

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

Flipped N/Q/H residues before XYZ refinement:
A  53 GLN
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 207 GLN
B 245 HIS
B 270 GLN
C  25 ASN
** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 225 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.046956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.036735 restraints weight = 75441.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.037819 restraints weight = 42669.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.038558 restraints weight = 28520.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
moved from start:          0.2746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  11871  Z= 0.214
  Angle     :  0.666   8.691  16116  Z= 0.338
  Chirality :  0.043   0.163   1861
  Planarity :  0.004   0.032   2063
  Dihedral  :  5.089  46.810   1644
  Min Nonbonded Distance : 1.856

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 14.38 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.21 (0.21), residues: 1498
  helix: -0.24 (0.20), residues: 681
  sheet: -2.47 (0.35), residues: 182
  loop : -2.52 (0.22), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 240 
 HIS   0.009   0.001   HIS B 263 
 PHE   0.015   0.002   PHE A 133 
 TYR   0.011   0.001   TYR C  86 
 ARG   0.007   0.000   ARG C 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03644 (  462)
  hydrogen bonds       : angle       4.53912 ( 1311)
  covalent geometry    : bond        0.00457 (11871)
  covalent geometry    : angle       0.66572 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 60
  time to evaluate  : 1.662 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.8877 (mmm) cc_final: 0.8573 (tpp)
REVERT: A  305 LYS cc_start: 0.9386 (mmtt) cc_final: 0.8769 (mmmm)
REVERT: A  334 LYS cc_start: 0.9284 (tttt) cc_final: 0.9030 (tttp)
REVERT: A  390 MET cc_start: 0.8718 (ptt) cc_final: 0.8271 (ptt)
REVERT: B   16 MET cc_start: 0.8215 (pmm) cc_final: 0.7666 (pmm)
REVERT: B  283 HIS cc_start: 0.9120 (m90) cc_final: 0.8680 (m90)
REVERT: C   16 MET cc_start: 0.8547 (tpt) cc_final: 0.8335 (tpt)
REVERT: D   81 GLU cc_start: 0.7191 (mp0) cc_final: 0.6985 (mp0)
REVERT: D  147 MET cc_start: 0.8550 (mmm) cc_final: 0.8230 (mmm)
REVERT: D  219 ASP cc_start: 0.8308 (m-30) cc_final: 0.8082 (m-30)
REVERT: D  222 ARG cc_start: 0.9137 (mtt180) cc_final: 0.8932 (mtm180)
REVERT: E   11 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8504 (mm-30)
REVERT: E  147 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7762 (mmm)
REVERT: E  187 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9222 (pp)
REVERT: E  219 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8614 (t0)
  outliers start: 27
  outliers final: 9
  residues processed: 83
  average time/residue: 0.3301
  time to fit residues: 40.8905
Evaluate side-chains
  68 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 2.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain D residue  260 ILE
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  147 MET
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  219 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 127 optimal weight:    6.9990
   chunk 79 optimal weight:    8.9990
   chunk 73 optimal weight:    4.9990
   chunk 93 optimal weight:    3.9990
   chunk 17 optimal weight:    6.9990
   chunk 11 optimal weight:    0.7980
   chunk 116 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 174 HIS
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 214 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.048024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.037890 restraints weight = 74121.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.038996 restraints weight = 41588.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.039740 restraints weight = 27707.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.2999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  11871  Z= 0.104
  Angle     :  0.554   8.862  16116  Z= 0.280
  Chirality :  0.041   0.149   1861
  Planarity :  0.003   0.031   2063
  Dihedral  :  4.728  38.980   1644
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 15.44 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.22), residues: 1498
  helix:  0.54 (0.21), residues: 681
  sheet: -2.35 (0.33), residues: 221
  loop : -2.25 (0.24), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A  45 
 HIS   0.005   0.001   HIS B 263 
 PHE   0.011   0.001   PHE E  64 
 TYR   0.009   0.001   TYR B  86 
 ARG   0.003   0.000   ARG B 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02989 (  462)
  hydrogen bonds       : angle       4.03009 ( 1311)
  covalent geometry    : bond        0.00230 (11871)
  covalent geometry    : angle       0.55390 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 64
  time to evaluate  : 1.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.8796 (mmm) cc_final: 0.8423 (tpp)
REVERT: A  125 MET cc_start: 0.8828 (mpp) cc_final: 0.8480 (mmp)
REVERT: A  209 MET cc_start: 0.8986 (mmm) cc_final: 0.8718 (mmm)
REVERT: A  305 LYS cc_start: 0.9376 (mmtt) cc_final: 0.8844 (mmmm)
REVERT: A  334 LYS cc_start: 0.9215 (tttt) cc_final: 0.8989 (tttp)
REVERT: A  390 MET cc_start: 0.8701 (ptt) cc_final: 0.8366 (ptp)
REVERT: B   16 MET cc_start: 0.7934 (pmm) cc_final: 0.7684 (pmm)
REVERT: B  283 HIS cc_start: 0.9015 (m90) cc_final: 0.8612 (m90)
REVERT: C   16 MET cc_start: 0.8644 (tpt) cc_final: 0.8391 (tpt)
REVERT: C  225 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8536 (pt)
REVERT: D   63 THR cc_start: 0.9257 (m) cc_final: 0.9002 (p)
REVERT: D  147 MET cc_start: 0.8670 (mmm) cc_final: 0.8369 (mmm)
REVERT: D  187 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8903 (pt)
REVERT: E  147 MET cc_start: 0.7960 (mmm) cc_final: 0.7678 (mmp)
REVERT: E  187 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9126 (pp)
REVERT: E  219 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8518 (t0)
REVERT: E  257 LEU cc_start: 0.9334 (mt) cc_final: 0.8965 (tt)
  outliers start: 19
  outliers final: 8
  residues processed: 81
  average time/residue: 0.2092
  time to fit residues: 25.8839
Evaluate side-chains
  71 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain D residue  187 LEU
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  219 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 115 optimal weight:    6.9990
   chunk 118 optimal weight:    1.9990
   chunk 71 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   chunk 128 optimal weight:    9.9990
   chunk 93 optimal weight:   10.0000
   chunk 124 optimal weight:    7.9990
   chunk 37 optimal weight:    0.7980
   chunk 75 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    3.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 283 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.046397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.036213 restraints weight = 76205.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.037265 restraints weight = 42980.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.037991 restraints weight = 28836.516|
|-----------------------------------------------------------------------------|
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.3319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11871  Z= 0.203
  Angle     :  0.622   8.204  16116  Z= 0.313
  Chirality :  0.043   0.142   1861
  Planarity :  0.003   0.029   2063
  Dihedral  :  4.797  39.911   1643
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 16.34 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.22), residues: 1498
  helix:  0.87 (0.21), residues: 683
  sheet: -2.30 (0.34), residues: 207
  loop : -2.16 (0.23), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  20 
 HIS   0.006   0.001   HIS B 194 
 PHE   0.014   0.002   PHE D 157 
 TYR   0.011   0.001   TYR B 293 
 ARG   0.003   0.000   ARG D 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03249 (  462)
  hydrogen bonds       : angle       4.20657 ( 1311)
  covalent geometry    : bond        0.00436 (11871)
  covalent geometry    : angle       0.62250 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 59
  time to evaluate  : 2.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.9071 (mmm) cc_final: 0.8647 (tpp)
REVERT: A  209 MET cc_start: 0.8920 (mmm) cc_final: 0.8639 (mmm)
REVERT: A  334 LYS cc_start: 0.9285 (tttt) cc_final: 0.9031 (tttp)
REVERT: A  390 MET cc_start: 0.8713 (ptt) cc_final: 0.8500 (ptt)
REVERT: B   16 MET cc_start: 0.8275 (pmm) cc_final: 0.7885 (pmm)
REVERT: B  283 HIS cc_start: 0.9137 (m-70) cc_final: 0.8674 (m90)
REVERT: C   16 MET cc_start: 0.8469 (tpt) cc_final: 0.8174 (tpt)
REVERT: D   63 THR cc_start: 0.9216 (m) cc_final: 0.8934 (p)
REVERT: D  187 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.8960 (pt)
REVERT: D  219 ASP cc_start: 0.8322 (m-30) cc_final: 0.8069 (m-30)
REVERT: E   11 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8603 (mm-30)
REVERT: E  147 MET cc_start: 0.7972 (mmm) cc_final: 0.7611 (mmp)
REVERT: E  187 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9245 (pp)
REVERT: E  219 ASP cc_start: 0.9018 (OUTLIER) cc_final: 0.8563 (t0)
REVERT: E  257 LEU cc_start: 0.9381 (mt) cc_final: 0.8982 (tt)
  outliers start: 21
  outliers final: 11
  residues processed: 77
  average time/residue: 0.2452
  time to fit residues: 30.8856
Evaluate side-chains
  69 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 1.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain B residue   46 MET
Chi-restraints excluded: chain B residue  129 TYR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain D residue  187 LEU
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  219 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 111 optimal weight:    0.9990
   chunk 50 optimal weight:    5.9990
   chunk 60 optimal weight:    6.9990
   chunk 90 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 55 optimal weight:    9.9990
   chunk 17 optimal weight:    6.9990
   chunk 129 optimal weight:    8.9990
   chunk 22 optimal weight:    1.9990
   chunk 34 optimal weight:    9.9990
   chunk 82 optimal weight:    0.8980
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.047031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.036893 restraints weight = 76155.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.037970 restraints weight = 42704.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.038699 restraints weight = 28515.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.3464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11871  Z= 0.139
  Angle     :  0.583  10.446  16116  Z= 0.287
  Chirality :  0.042   0.146   1861
  Planarity :  0.003   0.030   2063
  Dihedral  :  4.565  35.117   1642
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 17.40 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.22), residues: 1498
  helix:  1.20 (0.21), residues: 685
  sheet: -2.09 (0.34), residues: 229
  loop : -2.12 (0.24), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  20 
 HIS   0.005   0.001   HIS B 194 
 PHE   0.012   0.001   PHE D 157 
 TYR   0.009   0.001   TYR B 168 
 ARG   0.001   0.000   ARG D 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02926 (  462)
  hydrogen bonds       : angle       3.94271 ( 1311)
  covalent geometry    : bond        0.00304 (11871)
  covalent geometry    : angle       0.58274 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 60
  time to evaluate  : 1.220 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.9025 (mmm) cc_final: 0.8582 (tpp)
REVERT: A  105 MET cc_start: 0.8029 (tpp) cc_final: 0.7619 (tpp)
REVERT: A  209 MET cc_start: 0.9076 (mmm) cc_final: 0.8794 (mmm)
REVERT: A  334 LYS cc_start: 0.9257 (tttt) cc_final: 0.9029 (tttp)
REVERT: A  390 MET cc_start: 0.8663 (ptt) cc_final: 0.8368 (ptt)
REVERT: B   16 MET cc_start: 0.8104 (pmm) cc_final: 0.7845 (pmm)
REVERT: B  183 LEU cc_start: 0.9773 (OUTLIER) cc_final: 0.9440 (mt)
REVERT: B  283 HIS cc_start: 0.9063 (m-70) cc_final: 0.8660 (m90)
REVERT: C  295 MET cc_start: 0.8777 (mmm) cc_final: 0.8562 (mmm)
REVERT: D   63 THR cc_start: 0.9228 (m) cc_final: 0.8944 (p)
REVERT: D  147 MET cc_start: 0.8520 (mmm) cc_final: 0.8103 (mmt)
REVERT: D  187 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8874 (pt)
REVERT: D  219 ASP cc_start: 0.8270 (m-30) cc_final: 0.7960 (m-30)
REVERT: E   11 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8521 (mm-30)
REVERT: E  147 MET cc_start: 0.7944 (mmm) cc_final: 0.7675 (mmp)
REVERT: E  187 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9204 (pp)
REVERT: E  219 ASP cc_start: 0.8987 (OUTLIER) cc_final: 0.8485 (t0)
REVERT: E  257 LEU cc_start: 0.9324 (mt) cc_final: 0.8948 (tt)
  outliers start: 25
  outliers final: 12
  residues processed: 81
  average time/residue: 0.1989
  time to fit residues: 26.2211
Evaluate side-chains
  75 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 59
  time to evaluate  : 1.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain B residue  129 TYR
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain C residue  282 ILE
Chi-restraints excluded: chain D residue  110 LEU
Chi-restraints excluded: chain D residue  187 LEU
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue   66 MET
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  219 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 33 optimal weight:   10.0000
   chunk 109 optimal weight:    6.9990
   chunk 42 optimal weight:    9.9990
   chunk 112 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 119 optimal weight:    1.9990
   chunk 16 optimal weight:   10.0000
   chunk 107 optimal weight:    7.9990
   chunk 143 optimal weight:    7.9990
   chunk 29 optimal weight:    5.9990
   chunk 111 optimal weight:    3.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.046211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.036044 restraints weight = 77243.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.037053 restraints weight = 43489.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.037810 restraints weight = 29451.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.3665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  11871  Z= 0.198
  Angle     :  0.642  10.277  16116  Z= 0.314
  Chirality :  0.043   0.148   1861
  Planarity :  0.003   0.033   2063
  Dihedral  :  4.663  35.528   1642
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 18.38 %
    Favored  : 79.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.22), residues: 1498
  helix:  1.23 (0.21), residues: 687
  sheet: -2.06 (0.34), residues: 224
  loop : -2.07 (0.24), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  20 
 HIS   0.021   0.001   HIS B 263 
 PHE   0.014   0.002   PHE D 157 
 TYR   0.010   0.001   TYR D 268 
 ARG   0.002   0.000   ARG D 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03106 (  462)
  hydrogen bonds       : angle       4.15345 ( 1311)
  covalent geometry    : bond        0.00427 (11871)
  covalent geometry    : angle       0.64152 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 60
  time to evaluate  : 1.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.9101 (mmm) cc_final: 0.8699 (tpp)
REVERT: A  209 MET cc_start: 0.9102 (mmm) cc_final: 0.8843 (mmm)
REVERT: A  334 LYS cc_start: 0.9276 (tttt) cc_final: 0.9035 (tttp)
REVERT: A  390 MET cc_start: 0.8661 (ptt) cc_final: 0.8380 (ptp)
REVERT: B   16 MET cc_start: 0.8103 (pmm) cc_final: 0.7773 (pmm)
REVERT: B   46 MET cc_start: 0.8728 (mmm) cc_final: 0.8399 (tpt)
REVERT: B  283 HIS cc_start: 0.9011 (m-70) cc_final: 0.8621 (m90)
REVERT: D   63 THR cc_start: 0.9233 (m) cc_final: 0.8945 (p)
REVERT: D  187 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.8911 (pt)
REVERT: D  219 ASP cc_start: 0.8303 (m-30) cc_final: 0.7994 (m-30)
REVERT: E  147 MET cc_start: 0.7980 (mmm) cc_final: 0.7619 (mmp)
REVERT: E  168 VAL cc_start: 0.9451 (OUTLIER) cc_final: 0.9092 (p)
REVERT: E  187 LEU cc_start: 0.9669 (OUTLIER) cc_final: 0.9078 (pp)
REVERT: E  219 ASP cc_start: 0.9108 (OUTLIER) cc_final: 0.8532 (t0)
REVERT: E  257 LEU cc_start: 0.9346 (mt) cc_final: 0.8900 (tt)
  outliers start: 24
  outliers final: 17
  residues processed: 81
  average time/residue: 0.1908
  time to fit residues: 24.7497
Evaluate side-chains
  80 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 59
  time to evaluate  : 1.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain B residue  130 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  278 GLU
Chi-restraints excluded: chain C residue  282 ILE
Chi-restraints excluded: chain D residue   11 GLU
Chi-restraints excluded: chain D residue  110 LEU
Chi-restraints excluded: chain D residue  164 LEU
Chi-restraints excluded: chain D residue  187 LEU
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue   66 MET
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  168 VAL
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  219 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 61 optimal weight:    6.9990
   chunk 125 optimal weight:    9.9990
   chunk 41 optimal weight:    4.9990
   chunk 35 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 46 optimal weight:    0.7980
   chunk 113 optimal weight:    6.9990
   chunk 19 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 15 optimal weight:    9.9990
   chunk 13 optimal weight:    7.9990
   overall best weight:    4.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  82 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.045271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.035195 restraints weight = 79133.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.036240 restraints weight = 44402.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.036943 restraints weight = 29802.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.3960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040  11871  Z= 0.278
  Angle     :  0.732  10.352  16116  Z= 0.357
  Chirality :  0.045   0.152   1861
  Planarity :  0.004   0.035   2063
  Dihedral  :  4.924  33.155   1642
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 19.36 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.96 (0.22), residues: 1498
  helix:  1.08 (0.21), residues: 688
  sheet: -2.22 (0.34), residues: 217
  loop : -2.08 (0.24), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP E 211 
 HIS   0.012   0.001   HIS B 263 
 PHE   0.016   0.002   PHE D 157 
 TYR   0.012   0.002   TYR B 168 
 ARG   0.003   0.000   ARG D 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03414 (  462)
  hydrogen bonds       : angle       4.48470 ( 1311)
  covalent geometry    : bond        0.00592 (11871)
  covalent geometry    : angle       0.73196 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 57
  time to evaluate  : 1.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.9105 (mmm) cc_final: 0.8742 (tpp)
REVERT: A  209 MET cc_start: 0.9187 (mmm) cc_final: 0.8943 (mmm)
REVERT: A  334 LYS cc_start: 0.9319 (tttt) cc_final: 0.9065 (tttp)
REVERT: A  390 MET cc_start: 0.8694 (ptt) cc_final: 0.8428 (ptp)
REVERT: B   16 MET cc_start: 0.8189 (pmm) cc_final: 0.7634 (pmm)
REVERT: D   63 THR cc_start: 0.9238 (m) cc_final: 0.8946 (p)
REVERT: D  187 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.8953 (pt)
REVERT: D  219 ASP cc_start: 0.8340 (m-30) cc_final: 0.8108 (m-30)
REVERT: E  147 MET cc_start: 0.7975 (mmm) cc_final: 0.7599 (mmp)
REVERT: E  168 VAL cc_start: 0.9471 (OUTLIER) cc_final: 0.9073 (p)
REVERT: E  187 LEU cc_start: 0.9697 (OUTLIER) cc_final: 0.9262 (pp)
REVERT: E  219 ASP cc_start: 0.9209 (t0) cc_final: 0.8576 (t0)
  outliers start: 28
  outliers final: 17
  residues processed: 80
  average time/residue: 0.2045
  time to fit residues: 25.8445
Evaluate side-chains
  75 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 55
  time to evaluate  : 1.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain B residue  129 TYR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain C residue  282 ILE
Chi-restraints excluded: chain D residue  110 LEU
Chi-restraints excluded: chain D residue  164 LEU
Chi-restraints excluded: chain D residue  187 LEU
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue   66 MET
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  168 VAL
Chi-restraints excluded: chain E residue  187 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 82 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0070
   chunk 35 optimal weight:    1.9990
   chunk 11 optimal weight:    9.9990
   chunk 144 optimal weight:    7.9990
   chunk 84 optimal weight:    7.9990
   chunk 128 optimal weight:   10.0000
   chunk 27 optimal weight:    9.9990
   chunk 16 optimal weight:    6.9990
   chunk 10 optimal weight:    8.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    3.8006

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.045622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2761 r_free = 0.2761 target = 0.035583 restraints weight = 78296.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.036624 restraints weight = 43913.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.037343 restraints weight = 29398.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.4019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  11871  Z= 0.216
  Angle     :  0.674  11.071  16116  Z= 0.330
  Chirality :  0.043   0.142   1861
  Planarity :  0.003   0.038   2063
  Dihedral  :  4.833  33.546   1642
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 19.04 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.22), residues: 1498
  helix:  1.16 (0.21), residues: 690
  sheet: -2.24 (0.33), residues: 229
  loop : -1.97 (0.25), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 236 
 HIS   0.012   0.001   HIS B 263 
 PHE   0.015   0.002   PHE D 157 
 TYR   0.013   0.001   TYR B 168 
 ARG   0.002   0.000   ARG B 173 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03210 (  462)
  hydrogen bonds       : angle       4.32622 ( 1311)
  covalent geometry    : bond        0.00467 (11871)
  covalent geometry    : angle       0.67420 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 59
  time to evaluate  : 1.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.9090 (mmm) cc_final: 0.8708 (tpp)
REVERT: A  209 MET cc_start: 0.9183 (mmm) cc_final: 0.8912 (mmm)
REVERT: A  334 LYS cc_start: 0.9287 (tttt) cc_final: 0.9048 (tttp)
REVERT: B   16 MET cc_start: 0.8138 (pmm) cc_final: 0.7619 (pmm)
REVERT: B   46 MET cc_start: 0.8862 (mmm) cc_final: 0.8489 (tpt)
REVERT: D   63 THR cc_start: 0.9236 (m) cc_final: 0.8943 (p)
REVERT: D  187 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8937 (pt)
REVERT: D  219 ASP cc_start: 0.8380 (m-30) cc_final: 0.8179 (m-30)
REVERT: E  147 MET cc_start: 0.7962 (mmm) cc_final: 0.7613 (mmp)
REVERT: E  168 VAL cc_start: 0.9454 (OUTLIER) cc_final: 0.9073 (p)
REVERT: E  187 LEU cc_start: 0.9698 (OUTLIER) cc_final: 0.9256 (pp)
REVERT: E  219 ASP cc_start: 0.9201 (t0) cc_final: 0.8578 (t0)
REVERT: E  257 LEU cc_start: 0.9380 (mt) cc_final: 0.8963 (tt)
  outliers start: 26
  outliers final: 20
  residues processed: 82
  average time/residue: 0.1957
  time to fit residues: 25.6920
Evaluate side-chains
  78 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 55
  time to evaluate  : 1.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain B residue  129 TYR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain C residue  282 ILE
Chi-restraints excluded: chain D residue   11 GLU
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  110 LEU
Chi-restraints excluded: chain D residue  164 LEU
Chi-restraints excluded: chain D residue  187 LEU
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue   66 MET
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  168 VAL
Chi-restraints excluded: chain E residue  187 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 122 optimal weight:    0.3980
   chunk 46 optimal weight:    0.9990
   chunk 72 optimal weight:    0.5980
   chunk 132 optimal weight:    6.9990
   chunk 75 optimal weight:    2.9990
   chunk 71 optimal weight:    6.9990
   chunk 11 optimal weight:   20.0000
   chunk 25 optimal weight:   20.0000
   chunk 119 optimal weight:    0.7980
   chunk 133 optimal weight:    0.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
A  30 GLN
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.047500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.037648 restraints weight = 75591.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.038676 restraints weight = 42116.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.039434 restraints weight = 28211.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.4066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  11871  Z= 0.100
  Angle     :  0.600  11.839  16116  Z= 0.288
  Chirality :  0.042   0.205   1861
  Planarity :  0.003   0.038   2063
  Dihedral  :  4.420  29.221   1642
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 19.77 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.23), residues: 1498
  helix:  1.54 (0.21), residues: 687
  sheet: -1.95 (0.34), residues: 237
  loop : -1.87 (0.25), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 236 
 HIS   0.011   0.001   HIS B 263 
 PHE   0.009   0.001   PHE D 157 
 TYR   0.010   0.001   TYR B  86 
 ARG   0.002   0.000   ARG B 248 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02723 (  462)
  hydrogen bonds       : angle       3.81390 ( 1311)
  covalent geometry    : bond        0.00223 (11871)
  covalent geometry    : angle       0.59986 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 60
  time to evaluate  : 1.381 
Fit side-chains
REVERT: A   62 MET cc_start: 0.9020 (mmm) cc_final: 0.8640 (tpp)
REVERT: A  105 MET cc_start: 0.8103 (tpt) cc_final: 0.7866 (tpp)
REVERT: A  209 MET cc_start: 0.9188 (mmm) cc_final: 0.8930 (mmm)
REVERT: A  305 LYS cc_start: 0.9278 (mmtt) cc_final: 0.8948 (mmmt)
REVERT: A  334 LYS cc_start: 0.9185 (tttt) cc_final: 0.8977 (tttp)
REVERT: D   63 THR cc_start: 0.9198 (m) cc_final: 0.8901 (p)
REVERT: D  187 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8830 (pt)
REVERT: D  219 ASP cc_start: 0.8449 (m-30) cc_final: 0.8159 (m-30)
REVERT: E  147 MET cc_start: 0.7953 (mmm) cc_final: 0.7712 (mmp)
REVERT: E  168 VAL cc_start: 0.9259 (OUTLIER) cc_final: 0.8932 (p)
REVERT: E  187 LEU cc_start: 0.9652 (OUTLIER) cc_final: 0.9286 (pp)
REVERT: E  219 ASP cc_start: 0.9134 (t0) cc_final: 0.8522 (t0)
REVERT: E  257 LEU cc_start: 0.9206 (mt) cc_final: 0.8806 (tt)
  outliers start: 20
  outliers final: 11
  residues processed: 77
  average time/residue: 0.1918
  time to fit residues: 24.1670
Evaluate side-chains
  71 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 57
  time to evaluate  : 1.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain B residue  129 TYR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain C residue  282 ILE
Chi-restraints excluded: chain D residue  187 LEU
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  168 VAL
Chi-restraints excluded: chain E residue  187 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 68 optimal weight:   10.0000
   chunk 81 optimal weight:    5.9990
   chunk 89 optimal weight:    0.6980
   chunk 66 optimal weight:    8.9990
   chunk 22 optimal weight:   10.0000
   chunk 41 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 146 optimal weight:    8.9990
   chunk 75 optimal weight:    6.9990
   chunk 82 optimal weight:    0.8980
   chunk 121 optimal weight:    8.9990
   overall best weight:    3.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 196 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.045843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.035859 restraints weight = 77503.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.036896 restraints weight = 43627.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.037615 restraints weight = 29344.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.4149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  11871  Z= 0.204
  Angle     :  0.666  11.949  16116  Z= 0.322
  Chirality :  0.043   0.151   1861
  Planarity :  0.003   0.038   2063
  Dihedral  :  4.575  30.865   1642
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 20.26 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.23), residues: 1498
  helix:  1.44 (0.21), residues: 689
  sheet: -1.91 (0.34), residues: 232
  loop : -1.83 (0.25), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 211 
 HIS   0.010   0.001   HIS B 263 
 PHE   0.015   0.001   PHE D 157 
 TYR   0.010   0.001   TYR C  86 
 ARG   0.002   0.000   ARG D 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03095 (  462)
  hydrogen bonds       : angle       4.11604 ( 1311)
  covalent geometry    : bond        0.00442 (11871)
  covalent geometry    : angle       0.66615 (16116)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2972.62 seconds
wall clock time: 53 minutes 56.53 seconds (3236.53 seconds total)