Starting phenix.real_space_refine
on Tue Jul 29 21:37:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7o13_12688/07_2025/7o13_12688.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7o13_12688/07_2025/7o13_12688.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7o13_12688/07_2025/7o13_12688.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7o13_12688/07_2025/7o13_12688.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7o13_12688/07_2025/7o13_12688.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7o13_12688/07_2025/7o13_12688.cif"
  }
  resolution = 3.6
  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 50 residue(s): 0.04s

  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: 7.85, per 1000 atoms: 0.67
  Number of scatterers: 11651
  At special positions: 0
  Unit cell: (73.872, 92.016, 191.808, 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: 2.90
  Conformation dependent library (CDL) restraints added in 1.6 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
      47.2% alpha, 12.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 30 through 34
    Processing helix  chain 'A' and resid 344 through 348
      removed outlier: 4.322A  pdb=" N   GLY A 347 " --> pdb=" O   SER A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 383
      removed outlier: 3.745A  pdb=" N   LEU A 380 " --> pdb=" O   VAL A 376 " (cutoff:3.500A)
      removed outlier: 4.119A  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: 3.642A  pdb=" N   TRP A 400 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ARG A 403 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 50
      removed outlier: 3.804A  pdb=" N   ILE B  49 " --> pdb=" O   SER B  45 " (cutoff:3.500A)
      removed outlier: 3.594A  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: 3.549A  pdb=" N   LEU B  95 " --> pdb=" O   GLY B  91 " (cutoff:3.500A)
      removed outlier: 3.605A  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: 3.767A  pdb=" N   ALA B 142 " --> pdb=" O   GLY B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 178
      removed outlier: 3.694A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 172 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ARG B 177 " --> pdb=" O   ARG B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 192
      removed outlier: 4.013A  pdb=" N   VAL B 191 " --> pdb=" O   VAL B 187 " (cutoff:3.500A)
      removed outlier: 3.848A  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 237
    Processing helix  chain 'B' and resid 238 through 244
      removed outlier: 3.745A  pdb=" N   ASP B 242 " --> pdb=" O   GLN B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 275
      removed outlier: 3.718A  pdb=" N   LEU B 268 " --> pdb=" O   LYS B 264 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   ARG B 269 " --> pdb=" O   LEU B 265 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   GLN B 270 " --> pdb=" O   VAL B 266 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   LEU B 271 " --> pdb=" O   LEU B 267 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   GLY B 275 " --> pdb=" O   LEU B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 298
      removed outlier: 3.509A  pdb=" N   GLU B 296 " --> pdb=" O   ARG B 292 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ALA B 298 " --> pdb=" O   TYR B 294 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 41 through 50
      removed outlier: 3.784A  pdb=" N   SER C  45 " --> pdb=" O   GLY C  41 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ILE C  49 " --> pdb=" O   SER C  45 " (cutoff:3.500A)
      removed outlier: 3.515A  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
    Processing helix  chain 'C' and resid 105 through 109
    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 178
      removed outlier: 3.717A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 172 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 190 through 194
      removed outlier: 3.662A  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 240 through 244
      removed outlier: 3.794A  pdb=" N   ALA C 243 " --> pdb=" O   TRP C 240 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 263 through 274
      removed outlier: 3.551A  pdb=" N   LEU C 267 " --> pdb=" O   HIS C 263 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   LEU C 268 " --> pdb=" O   LYS C 264 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLU C 274 " --> pdb=" O   GLN C 270 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 286 through 299
      removed outlier: 3.857A  pdb=" N   GLU C 296 " --> pdb=" O   ARG C 292 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 15
      removed outlier: 3.551A  pdb=" N   ILE D   7 " --> pdb=" O   GLN D   3 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   LYS D  10 " --> pdb=" O   ASN D   6 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLU D  11 " --> pdb=" O   ILE D   7 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 18 through 42
      removed outlier: 3.583A  pdb=" N   ILE D  24 " --> pdb=" O   TRP D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 51 through 75
      removed outlier: 3.632A  pdb=" N   ALA D  56 " --> pdb=" O   PRO D  52 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LEU D  58 " --> pdb=" O   THR D  54 " (cutoff:3.500A)
      Proline residue:  D  67  - end of helix
      removed outlier: 3.599A  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: 3.668A  pdb=" N   LEU D  89 " --> pdb=" O   GLY D  85 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 98 through 129
      removed outlier: 4.064A  pdb=" N   LYS D 104 " --> pdb=" O   ILE D 100 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ILE D 111 " --> pdb=" O   GLY D 107 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   LEU D 117 " --> pdb=" O   ALA D 113 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ILE D 127 " --> pdb=" O   ALA D 123 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LEU D 129 " --> pdb=" O   LEU D 125 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 135 through 167
      removed outlier: 3.588A  pdb=" N   SER D 149 " --> pdb=" O   ARG D 145 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   THR D 151 " --> pdb=" O   MET D 147 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   LEU D 152 " --> pdb=" O   ILE D 148 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   VAL D 163 " --> pdb=" O   ALA D 159 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 170 through 188
      removed outlier: 3.670A  pdb=" N   GLY D 176 " --> pdb=" O   SER D 172 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL D 186 " --> pdb=" O   TRP D 182 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   VAL D 188 " --> pdb=" O   LEU D 184 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 188 through 200
      removed outlier: 3.549A  pdb=" N   SER D 200 " --> pdb=" O   LEU D 196 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 215
    Processing helix  chain 'D' and resid 216 through 226
      removed outlier: 3.522A  pdb=" N   ASN D 225 " --> pdb=" O   TYR D 221 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 236 through 244
      removed outlier: 3.581A  pdb=" N   SER D 240 " --> pdb=" O   GLY D 237 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA D 243 " --> pdb=" O   SER D 240 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 248 through 272
      removed outlier: 3.846A  pdb=" N   LEU D 252 " --> pdb=" O   PRO D 248 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   SER D 263 " --> pdb=" O   TRP D 259 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ALA D 267 " --> pdb=" O   SER D 263 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 3 through 7
      removed outlier: 3.604A  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: 3.567A  pdb=" N   GLU E  11 " --> pdb=" O   ILE E   7 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 18 through 41
      removed outlier: 3.565A  pdb=" N   ILE E  24 " --> pdb=" O   TRP E  20 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LEU E  38 " --> pdb=" O   GLY E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 52 through 75
      removed outlier: 3.812A  pdb=" N   SER E  57 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   MET E  66 " --> pdb=" O   ALA E  62 " (cutoff:3.500A)
      Proline residue:  E  67  - end of helix
      removed outlier: 3.515A  pdb=" N   TYR E  75 " --> pdb=" O   LEU E  71 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 78 through 85
    Processing helix  chain 'E' and resid 85 through 91
    Processing helix  chain 'E' and resid 96 through 120
      removed outlier: 3.507A  pdb=" N   ILE E 100 " --> pdb=" O   GLY E  96 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LEU E 101 " --> pdb=" O   ARG E  97 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ILE E 111 " --> pdb=" O   GLY E 107 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LEU E 112 " --> pdb=" O   HIS E 108 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   VAL E 116 " --> pdb=" O   LEU E 112 " (cutoff:3.500A)
      removed outlier: 4.253A  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: 3.743A  pdb=" N   LEU E 139 " --> pdb=" O   GLU E 135 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   TRP E 141 " --> pdb=" O   GLY E 137 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 143 through 168
    Processing helix  chain 'E' and resid 170 through 188
      removed outlier: 3.553A  pdb=" N   ALA E 175 " --> pdb=" O   LYS E 171 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLY E 180 " --> pdb=" O   GLY E 176 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   VAL E 186 " --> pdb=" O   TRP E 182 " (cutoff:3.500A)
      removed outlier: 3.811A  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
      removed outlier: 3.506A  pdb=" N   LEU E 212 " --> pdb=" O   LEU E 208 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 216 through 224
      removed outlier: 3.514A  pdb=" N   ILE E 224 " --> pdb=" O   ILE E 220 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 248 through 272
      removed outlier: 3.928A  pdb=" N   LEU E 252 " --> pdb=" O   PRO E 248 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   SER E 263 " --> pdb=" O   TRP E 259 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40
      removed outlier: 8.209A  pdb=" N   ARG A  44 " --> pdb=" O   PRO A  39 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   TRP A  45 " --> pdb=" O   ARG A  65 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58
      removed outlier: 6.470A  pdb=" N   GLY A 131 " --> pdb=" O   SER A 107 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ASP A 135 " --> pdb=" O   ILE A 111 " (cutoff:3.500A)
      removed outlier: 7.782A  pdb=" N   HIS A 163 " --> pdb=" O   PHE A 130 " (cutoff:3.500A)
      removed outlier: 5.952A  pdb=" N   VAL A 132 " --> pdb=" O   HIS A 163 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   PHE A 165 " --> pdb=" O   VAL A 132 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   VAL A 134 " --> pdb=" O   PHE A 165 " (cutoff:3.500A)
      removed outlier: 5.945A  pdb=" N   ILE A 162 " --> pdb=" O   TYR A 185 " (cutoff:3.500A)
      removed outlier: 7.503A  pdb=" N   ASP A 187 " --> pdb=" O   ILE A 162 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   LEU A 164 " --> pdb=" O   ASP A 187 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   ILE A 184 " --> pdb=" O   HIS A 207 " (cutoff:3.500A)
      removed outlier: 7.552A  pdb=" N   MET A 209 " --> pdb=" O   ILE A 184 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   ILE A 186 " --> pdb=" O   MET A 209 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   TYR A 204 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   ALA A 229 " --> pdb=" O   TYR A 204 " (cutoff:3.500A)
      removed outlier: 6.044A  pdb=" N   VAL A 206 " --> pdb=" O   ALA A 229 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   MET A 231 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 5.750A  pdb=" N   TYR A 208 " --> pdb=" O   MET A 231 " (cutoff:3.500A)
      removed outlier: 7.380A  pdb=" N   LEU A 252 " --> pdb=" O   THR A 226 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   TYR A 228 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   ASN A 254 " --> pdb=" O   TYR A 228 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   LEU A 230 " --> pdb=" O   ASN A 254 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   ILE A 251 " --> pdb=" O   PHE A 289 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   TYR A 291 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   MET A 253 " --> pdb=" O   TYR A 291 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   LEU A 288 " --> pdb=" O   HIS A 311 " (cutoff:3.500A)
      removed outlier: 6.851A  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: 6.286A  pdb=" N   ILE A 147 " --> pdb=" O   ARG A 178 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   VAL A 177 " --> pdb=" O   GLU A 200 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   ILE A 199 " --> pdb=" O   ARG A 222 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   THR A 221 " --> pdb=" O   GLU A 244 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   SER A 243 " --> pdb=" O   SER A 267 " (cutoff:3.500A)
      removed outlier: 6.492A  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: 6.604A  pdb=" N   VAL A  90 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
      removed outlier: 6.435A  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: 6.274A  pdb=" N   VAL B  18 " --> pdb=" O   ARG B  12 " (cutoff:3.500A)
      removed outlier: 7.282A  pdb=" N   ARG B  12 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   HIS B  20 " --> pdb=" O   SER B  10 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   SER B  10 " --> pdb=" O   HIS B  20 " (cutoff:3.500A)
      removed outlier: 5.813A  pdb=" N   LEU B  22 " --> pdb=" O   GLY B   8 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   GLY B   8 " --> pdb=" O   LEU B  22 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   VAL B   4 " --> pdb=" O   LEU B  26 " (cutoff:3.500A)
      removed outlier: 3.677A  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: 7.595A  pdb=" N   GLY B  77 " --> pdb=" O   LEU B 151 " (cutoff:3.500A)
      removed outlier: 7.952A  pdb=" N   ASP B 153 " --> pdb=" O   GLY B  77 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   LEU B  79 " --> pdb=" O   ASP B 153 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   LEU B 150 " --> pdb=" O   ILE B 182 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   CYS B 184 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   LEU B 152 " --> pdb=" O   CYS B 184 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   LEU B  32 " --> pdb=" O   LEU B 183 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 246 through 248
      removed outlier: 4.643A  pdb=" N   GLU B 256 " --> pdb=" O   ARG B 248 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ILE B 255 " --> pdb=" O   ALA B 227 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 22 through 25
      removed outlier: 5.722A  pdb=" N   LEU C  22 " --> pdb=" O   GLY C   8 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLY C   8 " --> pdb=" O   LEU C  22 " (cutoff:3.500A)
      removed outlier: 3.586A  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: 6.434A  pdb=" N   GLY C  77 " --> pdb=" O   LEU C 151 " (cutoff:3.500A)
      removed outlier: 7.296A  pdb=" N   ASP C 153 " --> pdb=" O   GLY C  77 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   LEU C  79 " --> pdb=" O   ASP C 153 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   LEU C  32 " --> pdb=" O   LEU C 183 " (cutoff:3.500A)
      removed outlier: 6.132A  pdb=" N   VAL C  31 " --> pdb=" O   ARG C 197 " (cutoff:3.500A)
      removed outlier: 7.562A  pdb=" N   ALA C 199 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   GLY C  33 " --> pdb=" O   ALA C 199 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   LEU C 201 " --> pdb=" O   GLY C  33 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   ALA C 198 " --> pdb=" O   VAL C 209 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   VAL C 209 " --> pdb=" O   ALA C 198 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   ILE C 200 " --> pdb=" O   GLN C 207 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 224 through 226
      removed outlier: 3.662A  pdb=" N   ILE C 225 " --> pdb=" O   VAL C 257 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ARG C 248 " --> pdb=" O   GLU C 256 " (cutoff:3.500A)

    473 hydrogen bonds defined for protein.
    1341 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.27

  Time building geometry restraints manager: 3.34 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 3506
        1.33 -     1.45: 1790
        1.45 -     1.57: 6507
        1.57 -     1.69: 4
        1.69 -     1.81: 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 1.09e+01
  bond pdb=" CB  VAL D 251 "
       pdb=" CG2 VAL D 251 "
    ideal  model  delta    sigma   weight residual
    1.521  1.448  0.073 3.30e-02 9.18e+02 4.91e+00
  bond pdb=" CA  ASN B  82 "
       pdb=" CB  ASN B  82 "
    ideal  model  delta    sigma   weight residual
    1.531  1.564 -0.033 1.51e-02 4.39e+03 4.79e+00
  bond pdb=" CG  GLU C  57 "
       pdb=" CD  GLU C  57 "
    ideal  model  delta    sigma   weight residual
    1.516  1.570 -0.054 2.50e-02 1.60e+03 4.58e+00
  bond pdb=" CA  ILE E  51 "
       pdb=" CB  ILE E  51 "
    ideal  model  delta    sigma   weight residual
    1.540  1.597 -0.057 2.70e-02 1.37e+03 4.46e+00
  ... (remaining 11866 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.55: 15806
        3.55 -     7.10: 273
        7.10 -    10.66: 32
       10.66 -    14.21: 4
       14.21 -    17.76: 1
  Bond angle restraints: 16116
  Sorted by residual:
  angle pdb=" C   LEU E 208 "
        pdb=" N   LEU E 209 "
        pdb=" CA  LEU E 209 "
      ideal   model   delta    sigma   weight residual
     120.06  126.71   -6.65 1.19e+00 7.06e-01 3.12e+01
  angle pdb=" CA  GLU A  42 "
        pdb=" CB  GLU A  42 "
        pdb=" CG  GLU A  42 "
      ideal   model   delta    sigma   weight residual
     114.10  125.21  -11.11 2.00e+00 2.50e-01 3.08e+01
  angle pdb=" CA  MET A 105 "
        pdb=" CB  MET A 105 "
        pdb=" CG  MET A 105 "
      ideal   model   delta    sigma   weight residual
     114.10  124.25  -10.15 2.00e+00 2.50e-01 2.58e+01
  angle pdb=" CA  LEU A  35 "
        pdb=" CB  LEU A  35 "
        pdb=" CG  LEU A  35 "
      ideal   model   delta    sigma   weight residual
     116.30  134.06  -17.76 3.50e+00 8.16e-02 2.58e+01
  angle pdb=" C   GLU B  81 "
        pdb=" N   ASN B  82 "
        pdb=" CA  ASN B  82 "
      ideal   model   delta    sigma   weight residual
     122.40  129.57   -7.17 1.45e+00 4.76e-01 2.45e+01
  ... (remaining 16111 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.74: 5919
       13.74 -    27.47: 788
       27.47 -    41.21: 248
       41.21 -    54.95: 48
       54.95 -    68.69: 18
  Dihedral angle restraints: 7021
    sinusoidal: 2752
      harmonic: 4269
  Sorted by residual:
  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 -156.96  -23.04     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" C   ASN B  82 "
           pdb=" N   ASN B  82 "
           pdb=" CA  ASN B  82 "
           pdb=" CB  ASN B  82 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.42   10.82     0      2.50e+00 1.60e-01 1.87e+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 -158.62  -21.38     0      5.00e+00 4.00e-02 1.83e+01
  ... (remaining 7018 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.097: 1651
       0.097 -    0.195: 184
       0.195 -    0.292: 20
       0.292 -    0.390: 3
       0.390 -    0.487: 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   -2.14   -0.49 2.00e-01 2.50e+01 5.94e+00
  chirality pdb=" CB  VAL C 187 "
            pdb=" CA  VAL C 187 "
            pdb=" CG1 VAL C 187 "
            pdb=" CG2 VAL C 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.17   -0.46 2.00e-01 2.50e+01 5.38e+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    2.23    0.41 2.00e-01 2.50e+01 4.27e+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   3.61e-02 1.30e+01
        pdb=" C   GLU B  81 "    0.062 2.00e-02 2.50e+03
        pdb=" O   GLU B  81 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   ASN B  82 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET D  66 "   -0.050 5.00e-02 4.00e+02   7.43e-02 8.84e+00
        pdb=" N   PRO D  67 "    0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO D  67 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO D  67 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET E  66 "    0.049 5.00e-02 4.00e+02   7.34e-02 8.63e+00
        pdb=" N   PRO E  67 "   -0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO E  67 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO E  67 "    0.042 5.00e-02 4.00e+02
  ... (remaining 2060 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 84
        2.53 -     3.12: 7505
        3.12 -     3.72: 18245
        3.72 -     4.31: 25588
        4.31 -     4.90: 42328
  Nonbonded interactions: 93750
  Sorted by model distance:
  nonbonded pdb="MG    MG A 501 "
            pdb=" O   HOH A 601 "
     model   vdw
     1.938 2.170
  nonbonded pdb=" OD1 ASP A 359 "
            pdb="MG    MG A 501 "
     model   vdw
     2.019 2.170
  nonbonded pdb=" OD1 ASP A 363 "
            pdb="MG    MG A 501 "
     model   vdw
     2.185 2.170
  nonbonded pdb=" OD1 ASN A 361 "
            pdb="MG    MG A 501 "
     model   vdw
     2.240 2.170
  nonbonded pdb=" O   SER A 293 "
            pdb=" OG  SER A 316 "
     model   vdw
     2.318 3.040
  ... (remaining 93745 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:             0.680
  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:             0.020
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     30.720
  Find NCS groups from input model:        0.520
  Set up NCS constraints:                  0.070
  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:3.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.074  11871  Z= 0.301
  Angle     :  1.117  17.761  16116  Z= 0.596
  Chirality :  0.066   0.487   1861
  Planarity :  0.007   0.074   2063
  Dihedral  : 14.308  68.687   4299
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  8.50 %
    Favored  : 90.69 %
  Cbeta Deviations :  0.07 %
  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: -5.71 (0.15), residues: 1498
  helix: -4.62 (0.07), residues: 645
  sheet: -3.48 (0.31), residues: 184
  loop : -2.80 (0.20), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP E 155 
 HIS   0.011   0.002   HIS C  37 
 PHE   0.020   0.002   PHE E  64 
 TYR   0.014   0.002   TYR C  13 
 ARG   0.009   0.001   ARG A 203 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.31261 (  473)
  hydrogen bonds       : angle      10.87483 ( 1341)
  covalent geometry    : bond        0.00668 (11871)
  covalent geometry    : angle       1.11747 (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
  123 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 1.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  209 MET cc_start: 0.9013 (mmm) cc_final: 0.8791 (mmm)
REVERT: A  231 MET cc_start: 0.9168 (mtt) cc_final: 0.8949 (mtm)
REVERT: A  235 LYS cc_start: 0.9431 (mmtt) cc_final: 0.9085 (tppp)
REVERT: A  305 LYS cc_start: 0.9165 (mmtt) cc_final: 0.8497 (mmmm)
REVERT: B  131 LYS cc_start: 0.9518 (tptt) cc_final: 0.9274 (tptp)
REVERT: B  283 HIS cc_start: 0.9072 (m90) cc_final: 0.7959 (m90)
REVERT: B  295 MET cc_start: 0.9345 (mmp) cc_final: 0.9083 (mmm)
REVERT: C  110 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8398 (t0)
REVERT: D   66 MET cc_start: 0.9229 (mmm) cc_final: 0.8796 (mmp)
REVERT: D  153 LEU cc_start: 0.8978 (tp) cc_final: 0.8766 (tt)
REVERT: D  169 ASN cc_start: 0.8830 (p0) cc_final: 0.8434 (m110)
REVERT: D  201 GLU cc_start: 0.9288 (mt-10) cc_final: 0.9079 (mm-30)
REVERT: D  219 ASP cc_start: 0.8957 (m-30) cc_final: 0.8541 (m-30)
REVERT: E   10 LYS cc_start: 0.8955 (tmtt) cc_final: 0.8719 (tmtt)
REVERT: E   83 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8384 (mt-10)
  outliers start: 10
  outliers final: 5
  residues processed: 123
  average time/residue: 0.3127
  time to fit residues: 52.9235
Evaluate side-chains
  84 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 1.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain C residue  110 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 124 optimal weight:    3.9990
   chunk 112 optimal weight:    0.9990
   chunk 62 optimal weight:    9.9990
   chunk 38 optimal weight:    7.9990
   chunk 75 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   chunk 116 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 70 optimal weight:    0.8980
   chunk 86 optimal weight:    3.9990
   chunk 134 optimal weight:    0.8980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A  30 GLN
A  77 GLN
A 123 ASN
A 141 GLN
A 145 ASN
A 160 ASN
A 175 ASN
A 176 HIS
A 190 ASN
A 207 HIS
A 212 ASN
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 301 ASN
A 324 ASN
A 341 GLN
B  11 GLN
B  20 HIS
B 176 GLN
B 270 GLN
** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 194 HIS
C 238 GLN
D 205 ASN
D 225 ASN
E 108 HIS
E 225 ASN

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.062799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.047519 restraints weight = 50685.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.049081 restraints weight = 25673.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.050124 restraints weight = 16421.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.1993

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= 0.116
  Angle     :  0.587   7.868  16116  Z= 0.304
  Chirality :  0.042   0.166   1861
  Planarity :  0.005   0.042   2063
  Dihedral  :  5.083  26.292   1649
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 12.34 %
    Favored  : 86.27 %
  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: -3.60 (0.18), residues: 1498
  helix: -2.05 (0.16), residues: 655
  sheet: -2.98 (0.33), residues: 182
  loop : -2.43 (0.22), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 253 
 HIS   0.014   0.001   HIS B 263 
 PHE   0.009   0.001   PHE D 157 
 TYR   0.016   0.001   TYR C  13 
 ARG   0.004   0.000   ARG D 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03824 (  473)
  hydrogen bonds       : angle       4.79146 ( 1341)
  covalent geometry    : bond        0.00250 (11871)
  covalent geometry    : angle       0.58748 (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
  107 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 1.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8606 (mpp) cc_final: 0.7981 (mpp)
REVERT: A  209 MET cc_start: 0.8965 (mmm) cc_final: 0.8550 (mmm)
REVERT: A  231 MET cc_start: 0.8870 (mtt) cc_final: 0.8552 (mtm)
REVERT: A  305 LYS cc_start: 0.9216 (mmtt) cc_final: 0.8485 (mmmm)
REVERT: A  334 LYS cc_start: 0.9354 (tttt) cc_final: 0.8817 (ttmp)
REVERT: B  184 CYS cc_start: 0.7111 (m) cc_final: 0.6672 (m)
REVERT: B  226 ARG cc_start: 0.7668 (ttm170) cc_final: 0.7277 (tpt170)
REVERT: B  283 HIS cc_start: 0.9039 (m90) cc_final: 0.8799 (m170)
REVERT: B  295 MET cc_start: 0.9407 (mmp) cc_final: 0.9158 (mmm)
REVERT: D   88 MET cc_start: 0.8352 (tpp) cc_final: 0.8088 (tpp)
REVERT: D  201 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8858 (mm-30)
REVERT: D  219 ASP cc_start: 0.8802 (m-30) cc_final: 0.8319 (m-30)
REVERT: E   66 MET cc_start: 0.9121 (mmm) cc_final: 0.8873 (mmp)
REVERT: E   83 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8318 (mt-10)
REVERT: E  187 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9100 (pp)
  outliers start: 17
  outliers final: 8
  residues processed: 103
  average time/residue: 0.2766
  time to fit residues: 40.8318
Evaluate side-chains
  78 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 1.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain C residue   13 TYR
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:    0.9990
   chunk 132 optimal weight:    5.9990
   chunk 55 optimal weight:    8.9990
   chunk 77 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0040
   chunk 64 optimal weight:    7.9990
   chunk 72 optimal weight:    8.9990
   chunk 102 optimal weight:    6.9990
   chunk 84 optimal weight:    0.9990
   chunk 98 optimal weight:    4.9990
   chunk 94 optimal weight:    0.7980
   overall best weight:    1.1598

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 115 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.062033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.046624 restraints weight = 52566.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.048154 restraints weight = 26839.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.049212 restraints weight = 17377.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.2436

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= 0.114
  Angle     :  0.546   6.777  16116  Z= 0.279
  Chirality :  0.042   0.152   1861
  Planarity :  0.004   0.036   2063
  Dihedral  :  4.637  23.319   1646
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 14.05 %
    Favored  : 84.64 %
  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: -2.15 (0.21), residues: 1498
  helix: -0.25 (0.20), residues: 668
  sheet: -2.67 (0.32), residues: 210
  loop : -2.21 (0.24), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 236 
 HIS   0.016   0.001   HIS B 263 
 PHE   0.010   0.001   PHE D 157 
 TYR   0.017   0.001   TYR B  86 
 ARG   0.003   0.000   ARG D 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03061 (  473)
  hydrogen bonds       : angle       4.08575 ( 1341)
  covalent geometry    : bond        0.00252 (11871)
  covalent geometry    : angle       0.54627 (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
  91 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 1.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 MET cc_start: 0.8583 (mmm) cc_final: 0.8294 (mpp)
REVERT: A  125 MET cc_start: 0.8890 (mpp) cc_final: 0.8250 (mpp)
REVERT: A  209 MET cc_start: 0.8885 (mmm) cc_final: 0.8474 (mmm)
REVERT: A  231 MET cc_start: 0.8810 (mtt) cc_final: 0.8524 (mtm)
REVERT: A  305 LYS cc_start: 0.9275 (mmtt) cc_final: 0.8826 (mmmm)
REVERT: A  334 LYS cc_start: 0.9346 (tttt) cc_final: 0.8805 (ttmp)
REVERT: B  283 HIS cc_start: 0.9080 (m90) cc_final: 0.8771 (m170)
REVERT: B  295 MET cc_start: 0.9404 (mmp) cc_final: 0.9132 (mmm)
REVERT: C  225 ILE cc_start: 0.7462 (OUTLIER) cc_final: 0.7166 (mp)
REVERT: D   11 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8317 (mm-30)
REVERT: D   81 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8154 (mt-10)
REVERT: D  201 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8857 (mm-30)
REVERT: D  219 ASP cc_start: 0.8742 (m-30) cc_final: 0.8238 (m-30)
REVERT: D  255 CYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8457 (t)
REVERT: E   10 LYS cc_start: 0.8887 (tmtt) cc_final: 0.8330 (tmtt)
REVERT: E  187 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9053 (pp)
  outliers start: 16
  outliers final: 9
  residues processed: 86
  average time/residue: 0.3105
  time to fit residues: 39.1103
Evaluate side-chains
  79 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 1.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain C residue   13 TYR
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain D residue  255 CYS
Chi-restraints excluded: chain E residue  187 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 72 optimal weight:    6.9990
   chunk 59 optimal weight:    9.9990
   chunk 18 optimal weight:   10.0000
   chunk 127 optimal weight:    6.9990
   chunk 79 optimal weight:    6.9990
   chunk 73 optimal weight:    3.9990
   chunk 93 optimal weight:   20.0000
   chunk 17 optimal weight:    0.9990
   chunk 11 optimal weight:   10.0000
   chunk 116 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  63 GLN
** A 241 ASN ** 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 = 0.3308 r_free = 0.3308 target = 0.058252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.043025 restraints weight = 53997.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.044423 restraints weight = 28238.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.045377 restraints weight = 18549.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.2937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.057  11871  Z= 0.304
  Angle     :  0.724   9.294  16116  Z= 0.358
  Chirality :  0.046   0.167   1861
  Planarity :  0.004   0.036   2063
  Dihedral  :  4.937  35.457   1646
  Min Nonbonded Distance : 1.797

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 15.93 %
    Favored  : 82.19 %
  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: -1.43 (0.22), residues: 1498
  helix:  0.51 (0.21), residues: 672
  sheet: -2.30 (0.34), residues: 217
  loop : -2.08 (0.24), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E  20 
 HIS   0.010   0.001   HIS B 263 
 PHE   0.016   0.002   PHE D 157 
 TYR   0.014   0.002   TYR C  13 
 ARG   0.006   0.001   ARG C 292 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03623 (  473)
  hydrogen bonds       : angle       4.48051 ( 1341)
  covalent geometry    : bond        0.00662 (11871)
  covalent geometry    : angle       0.72381 (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
  88 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 65
  time to evaluate  : 1.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 TRP cc_start: 0.8647 (m100) cc_final: 0.8408 (m100)
REVERT: A   62 MET cc_start: 0.8670 (mmm) cc_final: 0.8383 (tpp)
REVERT: A  125 MET cc_start: 0.8871 (mpp) cc_final: 0.8208 (mpp)
REVERT: A  209 MET cc_start: 0.8715 (mmm) cc_final: 0.8439 (mmm)
REVERT: A  231 MET cc_start: 0.8812 (mtt) cc_final: 0.8604 (mtt)
REVERT: A  305 LYS cc_start: 0.9386 (mmtt) cc_final: 0.8813 (mmmm)
REVERT: B  283 HIS cc_start: 0.9038 (m90) cc_final: 0.8633 (m170)
REVERT: C  295 MET cc_start: 0.8919 (mmm) cc_final: 0.8673 (mmm)
REVERT: D   81 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8209 (mt-10)
REVERT: D  118 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8905 (tt)
REVERT: D  219 ASP cc_start: 0.8638 (m-30) cc_final: 0.8011 (m-30)
REVERT: D  255 CYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8712 (t)
REVERT: E   10 LYS cc_start: 0.8983 (tmtt) cc_final: 0.8431 (tmtt)
REVERT: E   66 MET cc_start: 0.9182 (tpp) cc_final: 0.8906 (mmp)
REVERT: E  187 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9071 (pp)
REVERT: E  219 ASP cc_start: 0.8972 (t0) cc_final: 0.8759 (t0)
  outliers start: 23
  outliers final: 12
  residues processed: 86
  average time/residue: 0.2230
  time to fit residues: 29.3958
Evaluate side-chains
  75 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 1.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  103 THR
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  177 VAL
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  184 CYS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain C residue   13 TYR
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  255 CYS
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  187 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 115 optimal weight:    0.9980
   chunk 118 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 30 optimal weight:    5.9990
   chunk 128 optimal weight:    0.9990
   chunk 93 optimal weight:   20.0000
   chunk 124 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   chunk 75 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 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 = 0.3344 r_free = 0.3344 target = 0.059634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.044204 restraints weight = 52715.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.045682 restraints weight = 26579.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.046692 restraints weight = 17210.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.3091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11871  Z= 0.157
  Angle     :  0.576   8.575  16116  Z= 0.288
  Chirality :  0.043   0.156   1861
  Planarity :  0.003   0.034   2063
  Dihedral  :  4.619  25.589   1646
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 17.32 %
    Favored  : 81.05 %
  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: -0.97 (0.22), residues: 1498
  helix:  1.02 (0.21), residues: 680
  sheet: -2.12 (0.34), residues: 220
  loop : -2.02 (0.24), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E  20 
 HIS   0.022   0.001   HIS B 263 
 PHE   0.014   0.001   PHE D 157 
 TYR   0.014   0.001   TYR C  13 
 ARG   0.003   0.000   ARG B 173 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03030 (  473)
  hydrogen bonds       : angle       3.99296 ( 1341)
  covalent geometry    : bond        0.00351 (11871)
  covalent geometry    : angle       0.57642 (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
  89 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 1.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8908 (mpp) cc_final: 0.8173 (mpp)
REVERT: A  209 MET cc_start: 0.8785 (mmm) cc_final: 0.8490 (mmm)
REVERT: A  231 MET cc_start: 0.8820 (mtt) cc_final: 0.8522 (mtt)
REVERT: A  305 LYS cc_start: 0.9348 (mmtt) cc_final: 0.8900 (mmmm)
REVERT: A  334 LYS cc_start: 0.9388 (tttt) cc_final: 0.8805 (ttmp)
REVERT: B  183 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9318 (mt)
REVERT: B  283 HIS cc_start: 0.9039 (m90) cc_final: 0.8639 (m170)
REVERT: C   47 LYS cc_start: 0.9484 (mtmt) cc_final: 0.9268 (mtmm)
REVERT: C  133 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8903 (mtm)
REVERT: D   81 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8157 (mt-10)
REVERT: D  138 MET cc_start: 0.8538 (tmm) cc_final: 0.8319 (tmm)
REVERT: D  219 ASP cc_start: 0.8649 (m-30) cc_final: 0.8173 (m-30)
REVERT: D  255 CYS cc_start: 0.9029 (m) cc_final: 0.8803 (t)
REVERT: E   10 LYS cc_start: 0.8980 (tmtt) cc_final: 0.8414 (tmtt)
REVERT: E   81 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7731 (mt-10)
REVERT: E  187 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9098 (pp)
REVERT: E  219 ASP cc_start: 0.8994 (t0) cc_final: 0.8505 (t0)
  outliers start: 20
  outliers final: 12
  residues processed: 86
  average time/residue: 0.2318
  time to fit residues: 30.0261
Evaluate side-chains
  80 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 1.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  103 THR
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  177 VAL
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain C residue   13 TYR
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  184 CYS
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  187 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 111 optimal weight:    6.9990
   chunk 50 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9990
   chunk 52 optimal weight:    6.9990
   chunk 55 optimal weight:    0.0470
   chunk 17 optimal weight:    0.9990
   chunk 129 optimal weight:    8.9990
   chunk 22 optimal weight:    9.9990
   chunk 34 optimal weight:    6.9990
   chunk 82 optimal weight:    0.8980
   overall best weight:    1.3884

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.060157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.044933 restraints weight = 53519.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.046376 restraints weight = 27678.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.047370 restraints weight = 18086.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.3314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11871  Z= 0.117
  Angle     :  0.540   7.994  16116  Z= 0.268
  Chirality :  0.042   0.155   1861
  Planarity :  0.003   0.033   2063
  Dihedral  :  4.410  23.307   1646
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 17.24 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.23), residues: 1498
  helix:  1.48 (0.22), residues: 675
  sheet: -2.18 (0.33), residues: 228
  loop : -1.83 (0.25), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E  37 
 HIS   0.008   0.001   HIS B 263 
 PHE   0.011   0.001   PHE D 157 
 TYR   0.014   0.001   TYR C  13 
 ARG   0.001   0.000   ARG D 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02766 (  473)
  hydrogen bonds       : angle       3.71499 ( 1341)
  covalent geometry    : bond        0.00264 (11871)
  covalent geometry    : angle       0.53971 (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
  94 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 70
  time to evaluate  : 1.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 MET cc_start: 0.8383 (mmm) cc_final: 0.7955 (mpp)
REVERT: A  125 MET cc_start: 0.8975 (mpp) cc_final: 0.8300 (mpp)
REVERT: A  209 MET cc_start: 0.8738 (mmm) cc_final: 0.8436 (mmm)
REVERT: A  231 MET cc_start: 0.8822 (mtt) cc_final: 0.8506 (mtt)
REVERT: A  305 LYS cc_start: 0.9355 (mmtt) cc_final: 0.8745 (mmmm)
REVERT: A  334 LYS cc_start: 0.9359 (tttt) cc_final: 0.8773 (ttmp)
REVERT: B  183 LEU cc_start: 0.9617 (OUTLIER) cc_final: 0.9319 (mt)
REVERT: C  133 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8862 (mtm)
REVERT: C  295 MET cc_start: 0.8830 (mmm) cc_final: 0.8541 (mmm)
REVERT: D   81 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8110 (mt-10)
REVERT: D  138 MET cc_start: 0.8490 (tmm) cc_final: 0.8256 (tmm)
REVERT: D  219 ASP cc_start: 0.8629 (m-30) cc_final: 0.8148 (m-30)
REVERT: E   10 LYS cc_start: 0.8970 (tmtt) cc_final: 0.8466 (tmtt)
REVERT: E  187 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9103 (pp)
  outliers start: 24
  outliers final: 15
  residues processed: 91
  average time/residue: 0.2410
  time to fit residues: 32.3915
Evaluate side-chains
  79 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 61
  time to evaluate  : 1.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  103 THR
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  177 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  184 CYS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain C residue   13 TYR
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  184 CYS
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  187 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 109 optimal weight:    7.9990
   chunk 42 optimal weight:   10.0000
   chunk 112 optimal weight:    4.9990
   chunk 54 optimal weight:    0.4980
   chunk 119 optimal weight:    6.9990
   chunk 16 optimal weight:   20.0000
   chunk 107 optimal weight:    0.9980
   chunk 143 optimal weight:   20.0000
   chunk 29 optimal weight:    8.9990
   chunk 111 optimal weight:    6.9990
   overall best weight:    4.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 292 ASN
B 135 GLN
B 207 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.057448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.041764 restraints weight = 55120.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.043169 restraints weight = 27208.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.044218 restraints weight = 17864.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.3567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  11871  Z= 0.272
  Angle     :  0.697   8.792  16116  Z= 0.339
  Chirality :  0.045   0.167   1861
  Planarity :  0.003   0.031   2063
  Dihedral  :  4.717  29.917   1646
  Min Nonbonded Distance : 1.868

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 17.89 %
    Favored  : 80.15 %
  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: -0.64 (0.23), residues: 1498
  helix:  1.37 (0.21), residues: 678
  sheet: -2.22 (0.33), residues: 230
  loop : -1.81 (0.25), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E  20 
 HIS   0.009   0.001   HIS B 245 
 PHE   0.015   0.001   PHE D 157 
 TYR   0.013   0.002   TYR C  13 
 ARG   0.004   0.000   ARG B 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03367 (  473)
  hydrogen bonds       : angle       4.22847 ( 1341)
  covalent geometry    : bond        0.00595 (11871)
  covalent geometry    : angle       0.69664 (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
  81 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 57
  time to evaluate  : 1.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8960 (mpp) cc_final: 0.8278 (mpp)
REVERT: A  209 MET cc_start: 0.8906 (mmm) cc_final: 0.8573 (mmm)
REVERT: A  231 MET cc_start: 0.8992 (mtt) cc_final: 0.8686 (mtt)
REVERT: A  305 LYS cc_start: 0.9500 (mmtt) cc_final: 0.9287 (mmmt)
REVERT: B  183 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9104 (mt)
REVERT: C  133 MET cc_start: 0.9446 (OUTLIER) cc_final: 0.9111 (mtm)
REVERT: C  295 MET cc_start: 0.8915 (mmm) cc_final: 0.8517 (mmm)
REVERT: D   11 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8153 (tm-30)
REVERT: D   81 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8420 (mt-10)
REVERT: D  219 ASP cc_start: 0.8892 (m-30) cc_final: 0.8195 (m-30)
REVERT: E   10 LYS cc_start: 0.9077 (tmtt) cc_final: 0.8622 (tmtt)
REVERT: E  187 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8990 (pp)
REVERT: E  219 ASP cc_start: 0.9234 (t0) cc_final: 0.8995 (t0)
  outliers start: 24
  outliers final: 15
  residues processed: 78
  average time/residue: 0.2232
  time to fit residues: 26.7276
Evaluate side-chains
  75 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 56
  time to evaluate  : 1.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  103 THR
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  177 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  184 CYS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain C residue   13 TYR
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  184 CYS
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain D residue   11 GLU
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  187 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 125 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 5 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9990
   chunk 113 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 13 optimal weight:    8.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 175 ASN
** A 241 ASN ** 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 = 0.3356 r_free = 0.3356 target = 0.059896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.044819 restraints weight = 53035.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.046260 restraints weight = 27340.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.047250 restraints weight = 17767.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.3622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11871  Z= 0.118
  Angle     :  0.564  10.301  16116  Z= 0.276
  Chirality :  0.042   0.225   1861
  Planarity :  0.003   0.030   2063
  Dihedral  :  4.424  22.001   1646
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 18.22 %
    Favored  : 79.98 %
  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: -0.38 (0.23), residues: 1498
  helix:  1.66 (0.22), residues: 676
  sheet: -2.02 (0.33), residues: 234
  loop : -1.79 (0.25), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 253 
 HIS   0.006   0.001   HIS B 245 
 PHE   0.012   0.001   PHE D 157 
 TYR   0.014   0.001   TYR C  13 
 ARG   0.004   0.000   ARG B 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02818 (  473)
  hydrogen bonds       : angle       3.69170 ( 1341)
  covalent geometry    : bond        0.00268 (11871)
  covalent geometry    : angle       0.56415 (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
  88 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 66
  time to evaluate  : 1.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8949 (mpp) cc_final: 0.8313 (mpp)
REVERT: A  209 MET cc_start: 0.8748 (mmm) cc_final: 0.8454 (mmm)
REVERT: A  231 MET cc_start: 0.8844 (mtt) cc_final: 0.8534 (mtt)
REVERT: A  305 LYS cc_start: 0.9390 (mmtt) cc_final: 0.8856 (mmmt)
REVERT: A  334 LYS cc_start: 0.9360 (tttt) cc_final: 0.8730 (ttmp)
REVERT: B   95 LEU cc_start: 0.9437 (mt) cc_final: 0.8973 (tp)
REVERT: B  183 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9311 (mt)
REVERT: C  133 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8836 (mtm)
REVERT: D   11 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8131 (tm-30)
REVERT: D   81 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8126 (mt-10)
REVERT: D  219 ASP cc_start: 0.8603 (m-30) cc_final: 0.8155 (m-30)
REVERT: E   10 LYS cc_start: 0.9002 (tmtt) cc_final: 0.8489 (tmtt)
REVERT: E  219 ASP cc_start: 0.8968 (t0) cc_final: 0.8475 (t0)
  outliers start: 22
  outliers final: 16
  residues processed: 84
  average time/residue: 0.2213
  time to fit residues: 28.2175
Evaluate side-chains
  80 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 61
  time to evaluate  : 1.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  103 THR
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  177 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  417 HIS
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain C residue   13 TYR
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  184 CYS
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain D residue   11 GLU
Chi-restraints excluded: chain E residue   92 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 11 optimal weight:    7.9990
   chunk 144 optimal weight:    3.9990
   chunk 84 optimal weight:    8.9990
   chunk 128 optimal weight:    9.9990
   chunk 27 optimal weight:    3.9990
   chunk 16 optimal weight:   10.0000
   chunk 10 optimal weight:    7.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.058026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.042540 restraints weight = 54538.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.044025 restraints weight = 27081.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.045070 restraints weight = 17383.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.3723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  11871  Z= 0.214
  Angle     :  0.647  10.621  16116  Z= 0.311
  Chirality :  0.043   0.170   1861
  Planarity :  0.003   0.029   2063
  Dihedral  :  4.536  28.257   1646
  Min Nonbonded Distance : 1.907

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 18.63 %
    Favored  : 79.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.23), residues: 1498
  helix:  1.61 (0.22), residues: 679
  sheet: -2.08 (0.33), residues: 234
  loop : -1.83 (0.25), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 240 
 HIS   0.008   0.001   HIS B 245 
 PHE   0.014   0.001   PHE D 157 
 TYR   0.013   0.001   TYR E  93 
 ARG   0.004   0.000   ARG B 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03112 (  473)
  hydrogen bonds       : angle       3.97971 ( 1341)
  covalent geometry    : bond        0.00475 (11871)
  covalent geometry    : angle       0.64747 (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
  79 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 58
  time to evaluate  : 1.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.8921 (tpp) cc_final: 0.8012 (tpp)
REVERT: A  105 MET cc_start: 0.8674 (mmm) cc_final: 0.8312 (mmm)
REVERT: A  125 MET cc_start: 0.8952 (mpp) cc_final: 0.8314 (mpp)
REVERT: A  209 MET cc_start: 0.8888 (mmm) cc_final: 0.8684 (mmm)
REVERT: A  231 MET cc_start: 0.9071 (mtt) cc_final: 0.8800 (mtt)
REVERT: A  305 LYS cc_start: 0.9502 (mmtt) cc_final: 0.9300 (mmmt)
REVERT: B  183 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9160 (mt)
REVERT: C  133 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.8991 (mtm)
REVERT: C  295 MET cc_start: 0.8867 (mmm) cc_final: 0.8603 (mmm)
REVERT: D   11 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.7994 (tm-30)
REVERT: D   81 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8347 (mt-10)
REVERT: D  219 ASP cc_start: 0.8865 (m-30) cc_final: 0.8316 (m-30)
REVERT: E   10 LYS cc_start: 0.9100 (tmtt) cc_final: 0.8614 (tmtt)
REVERT: E  187 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9031 (pp)
  outliers start: 21
  outliers final: 15
  residues processed: 75
  average time/residue: 0.2269
  time to fit residues: 26.3423
Evaluate side-chains
  76 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 57
  time to evaluate  : 1.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  103 THR
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  177 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain C residue   13 TYR
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  184 CYS
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain D residue   11 GLU
Chi-restraints excluded: chain E residue   92 THR
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:   20.0000
   chunk 122 optimal weight:    0.9980
   chunk 46 optimal weight:    5.9990
   chunk 72 optimal weight:    0.8980
   chunk 132 optimal weight:    0.9990
   chunk 75 optimal weight:    0.0170
   chunk 71 optimal weight:    0.8980
   chunk 11 optimal weight:   10.0000
   chunk 25 optimal weight:   10.0000
   chunk 119 optimal weight:    2.9990
   chunk 133 optimal weight:    0.9980
   overall best weight:    0.7618

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.060639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.045666 restraints weight = 52787.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.047106 restraints weight = 27133.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.048107 restraints weight = 17624.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.3795

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= 0.096
  Angle     :  0.562  11.570  16116  Z= 0.269
  Chirality :  0.041   0.151   1861
  Planarity :  0.003   0.030   2063
  Dihedral  :  4.255  21.175   1646
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 19.20 %
    Favored  : 79.33 %
  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: -0.21 (0.23), residues: 1498
  helix:  1.86 (0.22), residues: 674
  sheet: -2.07 (0.34), residues: 236
  loop : -1.70 (0.25), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  98 
 HIS   0.005   0.001   HIS A 193 
 PHE   0.011   0.001   PHE E 157 
 TYR   0.013   0.001   TYR C  13 
 ARG   0.003   0.000   ARG B 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02626 (  473)
  hydrogen bonds       : angle       3.52095 ( 1341)
  covalent geometry    : bond        0.00222 (11871)
  covalent geometry    : angle       0.56182 (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
  87 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 1.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.8537 (tpp) cc_final: 0.7665 (tpp)
REVERT: A  105 MET cc_start: 0.8457 (mmm) cc_final: 0.8135 (mmm)
REVERT: A  125 MET cc_start: 0.8945 (mpp) cc_final: 0.8331 (mpp)
REVERT: A  209 MET cc_start: 0.8666 (mmm) cc_final: 0.8384 (mmm)
REVERT: A  231 MET cc_start: 0.8831 (mtt) cc_final: 0.8552 (mtt)
REVERT: A  334 LYS cc_start: 0.9349 (tttt) cc_final: 0.8763 (ttmp)
REVERT: B  183 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9269 (mt)
REVERT: C  133 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8819 (mtm)
REVERT: C  295 MET cc_start: 0.8797 (mmm) cc_final: 0.8582 (mmm)
REVERT: D   11 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7983 (tm-30)
REVERT: D   26 LEU cc_start: 0.9243 (tp) cc_final: 0.9008 (tp)
REVERT: D   81 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8139 (mt-10)
REVERT: D  219 ASP cc_start: 0.8598 (m-30) cc_final: 0.8134 (m-30)
REVERT: E   10 LYS cc_start: 0.9017 (tmtt) cc_final: 0.8468 (tmtt)
REVERT: E  187 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9069 (pp)
REVERT: E  219 ASP cc_start: 0.8923 (t0) cc_final: 0.8442 (t0)
  outliers start: 18
  outliers final: 13
  residues processed: 84
  average time/residue: 0.2282
  time to fit residues: 29.4586
Evaluate side-chains
  80 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 1.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
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  177 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain C residue   13 TYR
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  184 CYS
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain D residue   11 GLU
Chi-restraints excluded: chain E residue   92 THR
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:    4.9990
   chunk 81 optimal weight:    0.8980
   chunk 89 optimal weight:    6.9990
   chunk 66 optimal weight:    0.0770
   chunk 22 optimal weight:    9.9990
   chunk 41 optimal weight:    4.9990
   chunk 10 optimal weight:    7.9990
   chunk 146 optimal weight:    3.9990
   chunk 75 optimal weight:    0.0670
   chunk 82 optimal weight:    0.9980
   chunk 121 optimal weight:    7.9990
   overall best weight:    1.2078

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.058243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.042354 restraints weight = 54096.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.043857 restraints weight = 26836.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.044874 restraints weight = 17132.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.3853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11871  Z= 0.112
  Angle     :  0.572  10.954  16116  Z= 0.274
  Chirality :  0.041   0.152   1861
  Planarity :  0.003   0.028   2063
  Dihedral  :  4.191  22.351   1646
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 19.44 %
    Favored  : 79.00 %
  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: -0.14 (0.23), residues: 1498
  helix:  1.91 (0.22), residues: 677
  sheet: -1.99 (0.34), residues: 237
  loop : -1.69 (0.25), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 240 
 HIS   0.005   0.001   HIS B 245 
 PHE   0.012   0.001   PHE D 157 
 TYR   0.013   0.001   TYR C  13 
 ARG   0.003   0.000   ARG B 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02682 (  473)
  hydrogen bonds       : angle       3.52131 ( 1341)
  covalent geometry    : bond        0.00258 (11871)
  covalent geometry    : angle       0.57191 (16116)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3493.47 seconds
wall clock time: 63 minutes 4.76 seconds (3784.76 seconds total)