Starting phenix.real_space_refine
on Wed Mar  4 07:03:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7o13_12688/03_2026/7o13_12688.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7o13_12688/03_2026/7o13_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_12688/03_2026/7o13_12688.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7o13_12688/03_2026/7o13_12688.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7o13_12688/03_2026/7o13_12688.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7o13_12688/03_2026/7o13_12688.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.98, per 1000 atoms: 0.26
  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: 1.05
  Conformation dependent library (CDL) restraints added in 617.1 milliseconds
  

  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: 0.35
  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: 1.86

  Time building geometry restraints manager: 1.40 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:                  0.010
  Normalize map: mean=0, sd=1:             0.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.000
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.540
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -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
 ARG   0.009   0.001   ARG A 203 
 TYR   0.014   0.002   TYR C  13 
 PHE   0.020   0.002   PHE E  64 
 TRP   0.017   0.002   TRP E 155 
 HIS   0.011   0.002   HIS C  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00668 (11871)
  covalent geometry    : angle       1.11747 (16116)
  hydrogen bonds       : bond        0.31261 (  473)
  hydrogen bonds       : angle      10.87483 ( 1341)

*********************** 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  : 0.436 
Fit side-chains
   revert: symmetry clash
   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: 0.9167 (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: 0.8524 (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: 0.8749 (OUTLIER) cc_final: 0.8399 (t0)
REVERT: D   66 MET cc_start: 0.9229 (mmm) cc_final: 0.8754 (mmp)
REVERT: D  169 ASN cc_start: 0.8831 (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: 0.8954 (tmtt) cc_final: 0.8718 (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: 0.1346
  time to fit residues: 22.8134
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  : 0.424 
-------------------------------------------------------------------------------
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 98 optimal weight:    3.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:   20.0000
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    8.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    1.1786

-------------------------------------------------------------------------------
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 = 0.3423 r_free = 0.3423 target = 0.062525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.047188 restraints weight = 51065.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.048732 restraints weight = 26002.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.049789 restraints weight = 16704.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.050380 restraints weight = 12326.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.050879 restraints weight = 10162.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.2075

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= 0.125
  Angle     :  0.589   7.761  16116  Z= 0.305
  Chirality :  0.042   0.163   1861
  Planarity :  0.005   0.042   2063
  Dihedral  :  5.070  26.121   1649
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 12.58 %
    Favored  : 86.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.53 (0.18), residues: 1498
  helix: -2.01 (0.16), residues: 649
  sheet: -2.91 (0.33), residues: 187
  loop : -2.38 (0.22), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 222 
 TYR   0.015   0.001   TYR C  13 
 PHE   0.008   0.001   PHE D 157 
 TRP   0.010   0.001   TRP D 253 
 HIS   0.014   0.001   HIS B 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (11871)
  covalent geometry    : angle       0.58879 (16116)
  hydrogen bonds       : bond        0.03597 (  473)
  hydrogen bonds       : angle       4.75495 ( 1341)

*********************** 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
  106 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8633 (mpp) cc_final: 0.7980 (mpp)
REVERT: A  209 MET cc_start: 0.8957 (mmm) cc_final: 0.8551 (mmm)
REVERT: A  231 MET cc_start: 0.8890 (mtt) cc_final: 0.8520 (mtm)
REVERT: A  305 LYS cc_start: 0.9228 (mmtt) cc_final: 0.8495 (mmmm)
REVERT: A  334 LYS cc_start: 0.9340 (tttt) cc_final: 0.8803 (ttmp)
REVERT: B  184 CYS cc_start: 0.7070 (m) cc_final: 0.6752 (m)
REVERT: B  283 HIS cc_start: 0.9023 (m90) cc_final: 0.8784 (m170)
REVERT: B  295 MET cc_start: 0.9404 (mmp) cc_final: 0.9114 (mmm)
REVERT: D   81 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8112 (mt-10)
REVERT: D   88 MET cc_start: 0.8349 (tpp) cc_final: 0.8077 (tpp)
REVERT: D  201 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8851 (mm-30)
REVERT: D  219 ASP cc_start: 0.8792 (m-30) cc_final: 0.8327 (m-30)
REVERT: E   66 MET cc_start: 0.9111 (mmm) cc_final: 0.8876 (mmp)
REVERT: E   83 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8282 (mt-10)
REVERT: E  187 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9116 (pp)
  outliers start: 16
  outliers final: 8
  residues processed: 103
  average time/residue: 0.1111
  time to fit residues: 16.6799
Evaluate side-chains
  77 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
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 33 optimal weight:    8.9990
   chunk 46 optimal weight:    8.9990
   chunk 96 optimal weight:    5.9990
   chunk 43 optimal weight:    6.9990
   chunk 51 optimal weight:    7.9990
   chunk 108 optimal weight:    6.9990
   chunk 135 optimal weight:    0.9990
   chunk 10 optimal weight:   10.0000
   chunk 45 optimal weight:    5.9990
   chunk 4 optimal weight:    7.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    5.1990

-------------------------------------------------------------------------------
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**
B 135 GLN
** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 214 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.058168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.042976 restraints weight = 53687.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.044358 restraints weight = 28019.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.045306 restraints weight = 18412.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.045851 restraints weight = 13902.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.046294 restraints weight = 11635.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.2818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.064  11871  Z= 0.340
  Angle     :  0.783   8.725  16116  Z= 0.390
  Chirality :  0.047   0.189   1861
  Planarity :  0.004   0.036   2063
  Dihedral  :  5.177  35.652   1646
  Min Nonbonded Distance : 1.800

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 15.69 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.09 (0.21), residues: 1498
  helix: -0.23 (0.20), residues: 669
  sheet: -2.48 (0.33), residues: 205
  loop : -2.23 (0.24), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 292 
 TYR   0.015   0.002   TYR D 162 
 PHE   0.019   0.002   PHE D 157 
 TRP   0.017   0.002   TRP E  20 
 HIS   0.014   0.002   HIS B 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00736 (11871)
  covalent geometry    : angle       0.78299 (16116)
  hydrogen bonds       : bond        0.03979 (  473)
  hydrogen bonds       : angle       4.77246 ( 1341)

*********************** 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
  88 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8808 (mpp) cc_final: 0.8189 (mpp)
REVERT: A  209 MET cc_start: 0.8705 (mmm) cc_final: 0.8417 (mmm)
REVERT: A  305 LYS cc_start: 0.9372 (mmtt) cc_final: 0.8722 (mmmm)
REVERT: B  226 ARG cc_start: 0.7952 (ttm170) cc_final: 0.7201 (tmm160)
REVERT: B  283 HIS cc_start: 0.9092 (m90) cc_final: 0.8662 (m170)
REVERT: D   11 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8150 (tp30)
REVERT: D   81 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8251 (mt-10)
REVERT: D  118 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.8860 (tt)
REVERT: D  219 ASP cc_start: 0.8693 (m-30) cc_final: 0.8106 (m-30)
REVERT: D  255 CYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8597 (t)
REVERT: E   64 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.8861 (t80)
REVERT: E  187 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9114 (pp)
  outliers start: 19
  outliers final: 9
  residues processed: 85
  average time/residue: 0.1081
  time to fit residues: 13.7507
Evaluate side-chains
  77 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
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 D residue  118 ILE
Chi-restraints excluded: chain D residue  164 LEU
Chi-restraints excluded: chain D residue  255 CYS
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue   92 THR
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 118 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 144 optimal weight:    0.9980
   chunk 107 optimal weight:    0.8980
   chunk 28 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 25 optimal weight:    9.9990
   chunk 27 optimal weight:    1.9990
   chunk 135 optimal weight:    7.9990
   chunk 5 optimal weight:   10.0000
   chunk 89 optimal weight:    2.9990
   overall best weight:    1.5584

-------------------------------------------------------------------------------
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 ** 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 = 0.3350 r_free = 0.3350 target = 0.059800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.044367 restraints weight = 53254.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.045873 restraints weight = 26683.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.046911 restraints weight = 17174.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.047468 restraints weight = 12753.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.047940 restraints weight = 10628.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.2951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11871  Z= 0.129
  Angle     :  0.565   9.145  16116  Z= 0.284
  Chirality :  0.042   0.152   1861
  Planarity :  0.003   0.035   2063
  Dihedral  :  4.746  25.274   1646
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 16.67 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.38 (0.22), residues: 1498
  helix:  0.61 (0.21), residues: 674
  sheet: -2.30 (0.33), residues: 220
  loop : -2.12 (0.24), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 222 
 TYR   0.014   0.001   TYR C  13 
 PHE   0.012   0.001   PHE D 157 
 TRP   0.007   0.001   TRP E  37 
 HIS   0.015   0.001   HIS B 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (11871)
  covalent geometry    : angle       0.56495 (16116)
  hydrogen bonds       : bond        0.03066 (  473)
  hydrogen bonds       : angle       4.07285 ( 1341)

*********************** 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
  90 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 72
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.8640 (mmm) cc_final: 0.8294 (tpp)
REVERT: A  125 MET cc_start: 0.8914 (mpp) cc_final: 0.8206 (mpp)
REVERT: A  231 MET cc_start: 0.8686 (mtm) cc_final: 0.8481 (mtm)
REVERT: A  305 LYS cc_start: 0.9351 (mmtt) cc_final: 0.8905 (mmmm)
REVERT: A  334 LYS cc_start: 0.9384 (tttt) cc_final: 0.8808 (ttmp)
REVERT: B   34 LEU cc_start: 0.9542 (mt) cc_final: 0.9280 (mt)
REVERT: B  283 HIS cc_start: 0.9037 (m90) cc_final: 0.8672 (m170)
REVERT: D   11 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8212 (tp30)
REVERT: D   81 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8099 (mt-10)
REVERT: D  138 MET cc_start: 0.8492 (tmm) cc_final: 0.8244 (tmm)
REVERT: D  219 ASP cc_start: 0.8725 (m-30) cc_final: 0.8269 (m-30)
REVERT: D  255 CYS cc_start: 0.8928 (m) cc_final: 0.8652 (t)
REVERT: E   10 LYS cc_start: 0.8898 (tmtt) cc_final: 0.8422 (tmtt)
REVERT: E  187 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9107 (pp)
REVERT: E  219 ASP cc_start: 0.8910 (t0) cc_final: 0.8395 (t0)
  outliers start: 18
  outliers final: 12
  residues processed: 87
  average time/residue: 0.1014
  time to fit residues: 13.3857
Evaluate side-chains
  76 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
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  187 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain C residue   13 TYR
Chi-restraints excluded: chain D residue  116 VAL
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 32 optimal weight:    6.9990
   chunk 139 optimal weight:    7.9990
   chunk 137 optimal weight:    0.0870
   chunk 49 optimal weight:    0.9980
   chunk 126 optimal weight:    6.9990
   chunk 45 optimal weight:    0.0980
   chunk 29 optimal weight:    6.9990
   chunk 19 optimal weight:    0.7980
   chunk 71 optimal weight:    7.9990
   chunk 73 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.5960

-------------------------------------------------------------------------------
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**
** C 115 GLN ** 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 = 0.3399 r_free = 0.3399 target = 0.061443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.046180 restraints weight = 52088.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.047683 restraints weight = 26175.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.048715 restraints weight = 16808.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.049269 restraints weight = 12432.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.049769 restraints weight = 10330.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.3213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  11871  Z= 0.093
  Angle     :  0.526   9.142  16116  Z= 0.263
  Chirality :  0.041   0.172   1861
  Planarity :  0.003   0.035   2063
  Dihedral  :  4.397  22.234   1646
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 17.40 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.77 (0.23), residues: 1498
  helix:  1.22 (0.21), residues: 669
  sheet: -2.07 (0.35), residues: 218
  loop : -1.88 (0.24), residues: 611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 222 
 TYR   0.014   0.001   TYR C  13 
 PHE   0.010   0.001   PHE D 157 
 TRP   0.007   0.001   TRP A  98 
 HIS   0.008   0.001   HIS B 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 (11871)
  covalent geometry    : angle       0.52612 (16116)
  hydrogen bonds       : bond        0.02623 (  473)
  hydrogen bonds       : angle       3.68533 ( 1341)

*********************** 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
  98 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 76
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 MET cc_start: 0.8378 (mmm) cc_final: 0.8014 (mpp)
REVERT: A  125 MET cc_start: 0.8970 (mpp) cc_final: 0.8301 (mpp)
REVERT: A  209 MET cc_start: 0.8641 (mmm) cc_final: 0.8125 (mmm)
REVERT: A  231 MET cc_start: 0.8557 (mtm) cc_final: 0.8155 (mtm)
REVERT: A  305 LYS cc_start: 0.9333 (mmtt) cc_final: 0.8875 (mmmm)
REVERT: A  334 LYS cc_start: 0.9313 (tttt) cc_final: 0.8903 (ttmp)
REVERT: B   95 LEU cc_start: 0.9404 (mt) cc_final: 0.8922 (tp)
REVERT: B  183 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9209 (mt)
REVERT: B  283 HIS cc_start: 0.9057 (m90) cc_final: 0.8725 (m170)
REVERT: D   11 GLU cc_start: 0.8529 (mm-30) cc_final: 0.7994 (tp30)
REVERT: D   81 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7986 (mt-10)
REVERT: D  138 MET cc_start: 0.8457 (tmm) cc_final: 0.8217 (tmm)
REVERT: D  219 ASP cc_start: 0.8636 (m-30) cc_final: 0.8165 (m-30)
REVERT: E   10 LYS cc_start: 0.8890 (tmtt) cc_final: 0.8508 (tmtt)
REVERT: E  187 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9119 (pp)
REVERT: E  219 ASP cc_start: 0.8824 (t0) cc_final: 0.8349 (t0)
  outliers start: 22
  outliers final: 11
  residues processed: 96
  average time/residue: 0.1019
  time to fit residues: 14.7901
Evaluate side-chains
  82 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
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 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 61 optimal weight:    4.9990
   chunk 98 optimal weight:    4.9990
   chunk 132 optimal weight:    2.9990
   chunk 137 optimal weight:    5.9990
   chunk 74 optimal weight:    0.8980
   chunk 136 optimal weight:    6.9990
   chunk 143 optimal weight:    8.9990
   chunk 107 optimal weight:    5.9990
   chunk 93 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   chunk 63 optimal weight:   20.0000
   overall best weight:    3.3788

-------------------------------------------------------------------------------
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 207 HIS
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 292 ASN
B 207 GLN
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.058458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.043121 restraints weight = 54290.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.044531 restraints weight = 28530.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.045500 restraints weight = 18849.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.046052 restraints weight = 14255.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.046453 restraints weight = 11984.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.3406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  11871  Z= 0.227
  Angle     :  0.649  11.014  16116  Z= 0.318
  Chirality :  0.044   0.162   1861
  Planarity :  0.003   0.031   2063
  Dihedral  :  4.595  29.596   1646
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 18.38 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.65 (0.23), residues: 1498
  helix:  1.31 (0.21), residues: 680
  sheet: -2.15 (0.33), residues: 230
  loop : -1.79 (0.25), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 145 
 TYR   0.013   0.001   TYR C  13 
 PHE   0.014   0.001   PHE D 157 
 TRP   0.010   0.001   TRP E  20 
 HIS   0.017   0.001   HIS B 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 (11871)
  covalent geometry    : angle       0.64867 (16116)
  hydrogen bonds       : bond        0.03225 (  473)
  hydrogen bonds       : angle       4.05622 ( 1341)

*********************** 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
  83 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 61
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 MET cc_start: 0.8485 (mmm) cc_final: 0.7965 (mpp)
REVERT: A  125 MET cc_start: 0.8911 (mpp) cc_final: 0.8266 (mpp)
REVERT: A  209 MET cc_start: 0.8775 (mmm) cc_final: 0.8474 (mmm)
REVERT: A  231 MET cc_start: 0.8770 (mtm) cc_final: 0.8490 (mtm)
REVERT: A  305 LYS cc_start: 0.9369 (mmtt) cc_final: 0.8910 (mmmm)
REVERT: B  183 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9257 (mt)
REVERT: C  133 MET cc_start: 0.9183 (mtm) cc_final: 0.8900 (mtm)
REVERT: C  295 MET cc_start: 0.8985 (mmm) cc_final: 0.8756 (mmm)
REVERT: D   81 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8065 (mt-10)
REVERT: D  138 MET cc_start: 0.8656 (tmm) cc_final: 0.8382 (tmm)
REVERT: D  219 ASP cc_start: 0.8623 (m-30) cc_final: 0.8047 (m-30)
REVERT: E   10 LYS cc_start: 0.8948 (tmtt) cc_final: 0.8390 (tmtt)
REVERT: E  187 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9109 (pp)
REVERT: E  219 ASP cc_start: 0.8944 (t0) cc_final: 0.8423 (t0)
  outliers start: 22
  outliers final: 16
  residues processed: 80
  average time/residue: 0.1022
  time to fit residues: 12.3261
Evaluate side-chains
  74 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 56
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
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  206 LEU
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain E residue   66 MET
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 116 optimal weight:    7.9990
   chunk 142 optimal weight:    5.9990
   chunk 16 optimal weight:   20.0000
   chunk 90 optimal weight:    0.0970
   chunk 10 optimal weight:    8.9990
   chunk 52 optimal weight:    6.9990
   chunk 11 optimal weight:    9.9990
   chunk 26 optimal weight:    9.9990
   chunk 93 optimal weight:   20.0000
   chunk 5 optimal weight:    0.5980
   chunk 67 optimal weight:    8.9990
   overall best weight:    4.3384

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

Flipped N/Q/H residues before XYZ refinement:
A  38 GLN
A 175 ASN
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.057170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.041635 restraints weight = 54672.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.043072 restraints weight = 27570.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.044091 restraints weight = 17878.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.044658 restraints weight = 13389.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.045117 restraints weight = 11247.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.3707

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= 0.282
  Angle     :  0.700   8.613  16116  Z= 0.343
  Chirality :  0.045   0.173   1861
  Planarity :  0.004   0.034   2063
  Dihedral  :  4.817  30.117   1646
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 18.14 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.67 (0.23), residues: 1498
  helix:  1.36 (0.21), residues: 676
  sheet: -2.20 (0.33), residues: 230
  loop : -1.84 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 175 
 TYR   0.013   0.002   TYR C  13 
 PHE   0.017   0.001   PHE D 157 
 TRP   0.012   0.001   TRP E  20 
 HIS   0.010   0.001   HIS B 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.00618 (11871)
  covalent geometry    : angle       0.70013 (16116)
  hydrogen bonds       : bond        0.03403 (  473)
  hydrogen bonds       : angle       4.27958 ( 1341)

*********************** 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
  95 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 60
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.9052 (mmm) cc_final: 0.8140 (tpp)
REVERT: A  125 MET cc_start: 0.8941 (mpp) cc_final: 0.8270 (mpp)
REVERT: A  305 LYS cc_start: 0.9513 (mmtt) cc_final: 0.9053 (mmmm)
REVERT: B  183 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9215 (mt)
REVERT: B  281 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.7012 (pm20)
REVERT: C  133 MET cc_start: 0.9414 (OUTLIER) cc_final: 0.9081 (mtm)
REVERT: C  295 MET cc_start: 0.8992 (mmm) cc_final: 0.8791 (mmm)
REVERT: D   81 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8327 (mt-10)
REVERT: D  118 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8798 (tt)
REVERT: D  138 MET cc_start: 0.8711 (tmm) cc_final: 0.8405 (tmm)
REVERT: D  219 ASP cc_start: 0.8819 (m-30) cc_final: 0.8141 (m-30)
REVERT: E   10 LYS cc_start: 0.9069 (tmtt) cc_final: 0.8565 (tmtt)
REVERT: E  187 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9085 (pp)
REVERT: E  219 ASP cc_start: 0.9196 (t0) cc_final: 0.8652 (t0)
  outliers start: 35
  outliers final: 20
  residues processed: 90
  average time/residue: 0.0998
  time to fit residues: 13.7199
Evaluate side-chains
  84 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 59
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
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   15 SER
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 B residue  281 GLU
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  206 LEU
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain E residue   26 LEU
Chi-restraints excluded: chain E residue   66 MET
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 121 optimal weight:    6.9990
   chunk 73 optimal weight:    0.6980
   chunk 123 optimal weight:    5.9990
   chunk 89 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9990
   chunk 2 optimal weight:    6.9990
   chunk 99 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 70 optimal weight:    0.2980
   overall best weight:    1.3986

-------------------------------------------------------------------------------
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 ** 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 = 0.3313 r_free = 0.3313 target = 0.059006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.043593 restraints weight = 53965.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.045087 restraints weight = 26629.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.046102 restraints weight = 17047.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.046770 restraints weight = 12729.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.047194 restraints weight = 10460.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.3730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11871  Z= 0.118
  Angle     :  0.566   9.349  16116  Z= 0.279
  Chirality :  0.042   0.225   1861
  Planarity :  0.003   0.031   2063
  Dihedral  :  4.480  22.619   1646
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 18.87 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.23), residues: 1498
  helix:  1.66 (0.22), residues: 678
  sheet: -1.89 (0.33), residues: 239
  loop : -1.82 (0.25), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 175 
 TYR   0.016   0.001   TYR B 291 
 PHE   0.011   0.001   PHE E 157 
 TRP   0.009   0.001   TRP D 253 
 HIS   0.006   0.001   HIS B 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (11871)
  covalent geometry    : angle       0.56617 (16116)
  hydrogen bonds       : bond        0.02853 (  473)
  hydrogen bonds       : angle       3.71823 ( 1341)

*********************** 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: 24
    poor density    : 64
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.8981 (mmm) cc_final: 0.8160 (tpp)
REVERT: A  105 MET cc_start: 0.8620 (mmm) cc_final: 0.8187 (mmm)
REVERT: A  125 MET cc_start: 0.8980 (mpp) cc_final: 0.8308 (mpp)
REVERT: A  305 LYS cc_start: 0.9425 (mmtt) cc_final: 0.9149 (mmmt)
REVERT: A  334 LYS cc_start: 0.9183 (tttt) cc_final: 0.8524 (ttmp)
REVERT: B   95 LEU cc_start: 0.9310 (mt) cc_final: 0.8797 (tp)
REVERT: B  183 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9207 (mt)
REVERT: B  281 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6944 (pm20)
REVERT: C  133 MET cc_start: 0.9327 (OUTLIER) cc_final: 0.8971 (mtm)
REVERT: D   81 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8247 (mt-10)
REVERT: D  138 MET cc_start: 0.8498 (tmm) cc_final: 0.8239 (tmm)
REVERT: D  219 ASP cc_start: 0.8815 (m-30) cc_final: 0.8263 (m-30)
REVERT: E   10 LYS cc_start: 0.9055 (tmtt) cc_final: 0.8558 (tmtt)
REVERT: E  219 ASP cc_start: 0.9192 (t0) cc_final: 0.8605 (t0)
  outliers start: 24
  outliers final: 18
  residues processed: 83
  average time/residue: 0.1015
  time to fit residues: 12.6248
Evaluate side-chains
  82 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 61
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
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   15 SER
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 B residue  281 GLU
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  206 LEU
Chi-restraints excluded: chain E residue   66 MET
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 4 optimal weight:   20.0000
   chunk 126 optimal weight:    6.9990
   chunk 109 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 74 optimal weight:    0.0020
   chunk 54 optimal weight:    4.9990
   chunk 139 optimal weight:    2.9990
   chunk 131 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   chunk 41 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    1.3394

-------------------------------------------------------------------------------
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 ** 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 = 0.3321 r_free = 0.3321 target = 0.059356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.043867 restraints weight = 53572.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.045362 restraints weight = 26914.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.046391 restraints weight = 17358.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.047036 restraints weight = 12954.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.047458 restraints weight = 10697.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.3821

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     :  0.579  12.000  16116  Z= 0.280
  Chirality :  0.042   0.182   1861
  Planarity :  0.003   0.032   2063
  Dihedral  :  4.336  23.560   1646
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 19.12 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.23), residues: 1498
  helix:  1.81 (0.22), residues: 674
  sheet: -1.80 (0.35), residues: 229
  loop : -1.74 (0.25), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 175 
 TYR   0.015   0.001   TYR B 291 
 PHE   0.011   0.001   PHE E 157 
 TRP   0.007   0.001   TRP A  45 
 HIS   0.006   0.001   HIS B 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (11871)
  covalent geometry    : angle       0.57923 (16116)
  hydrogen bonds       : bond        0.02754 (  473)
  hydrogen bonds       : angle       3.60492 ( 1341)

*********************** 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
  89 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 66
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.9004 (mmm) cc_final: 0.8254 (tpp)
REVERT: A  105 MET cc_start: 0.8603 (mmm) cc_final: 0.8230 (mmm)
REVERT: A  125 MET cc_start: 0.8983 (mpp) cc_final: 0.8346 (mpp)
REVERT: A  209 MET cc_start: 0.8793 (mmm) cc_final: 0.8446 (mmt)
REVERT: A  305 LYS cc_start: 0.9411 (mmtt) cc_final: 0.8882 (mmmt)
REVERT: A  334 LYS cc_start: 0.9182 (tttt) cc_final: 0.8528 (ttmp)
REVERT: B   95 LEU cc_start: 0.9356 (mt) cc_final: 0.8856 (tp)
REVERT: B  183 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9204 (mt)
REVERT: B  281 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7009 (pm20)
REVERT: C  133 MET cc_start: 0.9303 (OUTLIER) cc_final: 0.8931 (mtm)
REVERT: D   81 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8255 (mt-10)
REVERT: D  138 MET cc_start: 0.8476 (tmm) cc_final: 0.8232 (tmm)
REVERT: D  219 ASP cc_start: 0.8810 (m-30) cc_final: 0.8259 (m-30)
REVERT: E   10 LYS cc_start: 0.9104 (tmtt) cc_final: 0.8613 (tmtt)
REVERT: E   88 MET cc_start: 0.8917 (tpp) cc_final: 0.8636 (tpp)
REVERT: E  219 ASP cc_start: 0.9165 (t0) cc_final: 0.8592 (t0)
  outliers start: 23
  outliers final: 15
  residues processed: 84
  average time/residue: 0.1013
  time to fit residues: 12.8124
Evaluate side-chains
  83 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 65
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
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 A residue  417 HIS
Chi-restraints excluded: chain B residue   15 SER
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 B residue  281 GLU
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  206 LEU
Chi-restraints excluded: chain E residue   92 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 118 optimal weight:    5.9990
   chunk 73 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 127 optimal weight:    9.9990
   chunk 98 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 139 optimal weight:    4.9990
   chunk 50 optimal weight:    8.9990
   chunk 147 optimal weight:    0.8980
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 ** 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 = 0.3312 r_free = 0.3312 target = 0.058917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.043417 restraints weight = 54246.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.044904 restraints weight = 27222.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.045808 restraints weight = 17535.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.046548 restraints weight = 13297.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.046917 restraints weight = 10908.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.3860

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= 0.146
  Angle     :  0.588  10.350  16116  Z= 0.285
  Chirality :  0.042   0.162   1861
  Planarity :  0.003   0.032   2063
  Dihedral  :  4.358  25.120   1646
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 19.04 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.23), residues: 1498
  helix:  1.84 (0.22), residues: 678
  sheet: -1.76 (0.35), residues: 221
  loop : -1.80 (0.25), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 175 
 TYR   0.014   0.001   TYR B 291 
 PHE   0.012   0.001   PHE D 157 
 TRP   0.009   0.001   TRP C 240 
 HIS   0.006   0.001   HIS B 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (11871)
  covalent geometry    : angle       0.58843 (16116)
  hydrogen bonds       : bond        0.02846 (  473)
  hydrogen bonds       : angle       3.66828 ( 1341)

********************** 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
  83 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 62
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.9003 (mmm) cc_final: 0.8337 (tpp)
REVERT: A  105 MET cc_start: 0.8612 (mmm) cc_final: 0.8256 (mmm)
REVERT: A  125 MET cc_start: 0.8962 (mpp) cc_final: 0.8330 (mpp)
REVERT: A  305 LYS cc_start: 0.9487 (mmtt) cc_final: 0.8930 (mmmt)
REVERT: B   95 LEU cc_start: 0.9366 (mt) cc_final: 0.8860 (tp)
REVERT: B  183 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9197 (mt)
REVERT: B  281 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7074 (pm20)
REVERT: C  133 MET cc_start: 0.9311 (OUTLIER) cc_final: 0.8938 (mtm)
REVERT: D   81 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8272 (mt-10)
REVERT: D  138 MET cc_start: 0.8480 (tmm) cc_final: 0.8235 (tmm)
REVERT: D  219 ASP cc_start: 0.8767 (m-30) cc_final: 0.8055 (m-30)
REVERT: E   10 LYS cc_start: 0.9105 (tmtt) cc_final: 0.8629 (tmtt)
REVERT: E   88 MET cc_start: 0.8916 (tpp) cc_final: 0.8612 (tpp)
REVERT: E  219 ASP cc_start: 0.9176 (t0) cc_final: 0.8566 (t0)
  outliers start: 21
  outliers final: 17
  residues processed: 79
  average time/residue: 0.0897
  time to fit residues: 10.7473
Evaluate side-chains
  82 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 62
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
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 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 B residue  281 GLU
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  206 LEU
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain E residue   35 ILE
Chi-restraints excluded: chain E residue   66 MET
Chi-restraints excluded: chain E residue   92 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 113 optimal weight:    5.9990
   chunk 103 optimal weight:    8.9990
   chunk 85 optimal weight:    0.5980
   chunk 91 optimal weight:   10.0000
   chunk 8 optimal weight:    5.9990
   chunk 140 optimal weight:    5.9990
   chunk 47 optimal weight:    0.0980
   chunk 112 optimal weight:    0.8980
   chunk 94 optimal weight:    7.9990
   chunk 117 optimal weight:    0.9980
   chunk 142 optimal weight:    0.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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  82 ASN
** C 115 GLN ** 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 = 0.3378 r_free = 0.3378 target = 0.060608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.045621 restraints weight = 53001.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.047051 restraints weight = 27314.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.048035 restraints weight = 17754.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.048598 restraints weight = 13325.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.049045 restraints weight = 11111.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.3951

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= 0.095
  Angle     :  0.569  11.186  16116  Z= 0.274
  Chirality :  0.041   0.152   1861
  Planarity :  0.003   0.031   2063
  Dihedral  :  4.201  21.397   1646
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 19.77 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.23), residues: 1498
  helix:  1.99 (0.22), residues: 673
  sheet: -1.75 (0.34), residues: 238
  loop : -1.71 (0.25), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 175 
 TYR   0.016   0.001   TYR B 291 
 PHE   0.010   0.001   PHE E 157 
 TRP   0.009   0.001   TRP A  98 
 HIS   0.005   0.001   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 (11871)
  covalent geometry    : angle       0.56863 (16116)
  hydrogen bonds       : bond        0.02589 (  473)
  hydrogen bonds       : angle       3.42376 ( 1341)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1751.71 seconds
wall clock time: 31 minutes 11.08 seconds (1871.08 seconds total)