Starting phenix.real_space_refine
on Fri Feb 14 02:06:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z1v_39737/02_2025/8z1v_39737_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z1v_39737/02_2025/8z1v_39737.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8z1v_39737/02_2025/8z1v_39737.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z1v_39737/02_2025/8z1v_39737.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z1v_39737/02_2025/8z1v_39737_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z1v_39737/02_2025/8z1v_39737_neut.cif"
  }
  resolution = 3.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.022
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
     Fe      8      7.16       5
     S      74      5.16       5
     C    6139      2.51       5
     N    1658      2.21       5
     O    1683      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 75 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9562
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2380
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 14, 'TRANS': 291}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2122
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2122
          Classifications: {'peptide': 280}
          Link IDs: {'PTRANS': 14, 'TRANS': 265}
    Chain: "C"
      Number of atoms: 2481
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 323, 2481
          Classifications: {'peptide': 323}
          Link IDs: {'PTRANS': 20, 'TRANS': 302}
    Chain: "D"
      Number of atoms: 2563
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 325, 2563
          Classifications: {'peptide': 325}
          Link IDs: {'PTRANS': 23, 'TRANS': 301}
    Chain: "C"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Unusual residues: {'SF4': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Unusual residues: {'SF4': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   6711  SG  CYS C 290      22.078  31.180  99.809  1.00151.77           S
  ATOM   6663  SG  CYS C 284      18.109  34.615  95.541  1.00128.87           S
  ATOM   6903  SG  CYS C 315      17.616  35.255 102.133  1.00142.04           S
  ATOM   6767  SG  CYS C 297      15.308  30.150  99.252  1.00155.91           S
  ATOM   9218  SG  CYS D 293      66.298  56.997 100.668  1.00146.86           S
  ATOM   9264  SG  CYS D 299      61.661  59.918 104.969  1.00159.29           S
  ATOM   9325  SG  CYS D 306      68.298  61.053 105.064  1.00167.47           S
  ATOM   9454  SG  CYS D 323      65.448  55.497 107.415  1.00154.31           S

  Time building chain proxies: 6.10, per 1000 atoms: 0.64
  Number of scatterers: 9562
  At special positions: 0
  Unit cell: (93.6, 94.64, 126.88, 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)
     Fe      8     26.01
     S      74     16.00
     O    1683      8.00
     N    1658      7.00
     C    6139      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.39
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" SF4 C 401 "
        pdb="FE3  SF4 C 401 " - pdb=" SG  CYS C 315 "
        pdb="FE4  SF4 C 401 " - pdb=" SG  CYS C 297 "
        pdb="FE1  SF4 C 401 " - pdb=" SG  CYS C 290 "
        pdb="FE2  SF4 C 401 " - pdb=" SG  CYS C 284 "
      pdb=" SF4 D 401 "
        pdb="FE3  SF4 D 401 " - pdb=" SG  CYS D 306 "
        pdb="FE4  SF4 D 401 " - pdb=" SG  CYS D 323 "
        pdb="FE1  SF4 D 401 " - pdb=" SG  CYS D 293 "
        pdb="FE2  SF4 D 401 " - pdb=" SG  CYS D 299 "
      Number of angles added : 24


  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2268

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 5 sheets defined
      60.2% alpha, 10.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 29
      removed outlier: 3.943A  pdb=" N   LEU A   6 " --> pdb=" O   LEU A   2 " (cutoff:3.500A)
      Proline residue:  A  14  - end of helix
    Processing helix  chain 'A' and resid 63 through 76
      removed outlier: 3.936A  pdb=" N   LEU A  67 " --> pdb=" O   TRP A  63 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   HIS A  68 " --> pdb=" O   GLN A  64 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   HIS A  75 " --> pdb=" O   TRP A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 124
      Proline residue:  A  94  - end of helix
      removed outlier: 3.975A  pdb=" N   LEU A 102 " --> pdb=" O   ALA A  98 " (cutoff:3.500A)
      Proline residue:  A 116  - end of helix
    Processing helix  chain 'A' and resid 127 through 142
    Processing helix  chain 'A' and resid 144 through 157
    Processing helix  chain 'A' and resid 184 through 192
      removed outlier: 3.845A  pdb=" N   ALA A 190 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 232
      removed outlier: 4.731A  pdb=" N   LEU A 207 " --> pdb=" O   ALA A 203 " (cutoff:3.500A)
      Proline residue:  A 208  - end of helix
      removed outlier: 4.756A  pdb=" N   ILE A 215 " --> pdb=" O   VAL A 211 " (cutoff:3.500A)
      Proline residue:  A 216  - end of helix
    Processing helix  chain 'A' and resid 234 through 243
      removed outlier: 3.549A  pdb=" N   ARG A 238 " --> pdb=" O   GLU A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 254
    Processing helix  chain 'A' and resid 254 through 282
      removed outlier: 4.090A  pdb=" N   ASN A 258 " --> pdb=" O   HIS A 254 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   LEU A 261 " --> pdb=" O   ARG A 257 " (cutoff:3.500A)
      Proline residue:  A 262  - end of helix
      removed outlier: 3.514A  pdb=" N   THR A 265 " --> pdb=" O   LEU A 261 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   GLY A 272 " --> pdb=" O   GLY A 268 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   LEU A 275 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   ALA A 276 " --> pdb=" O   GLY A 272 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU A 280 " --> pdb=" O   ALA A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 301
      removed outlier: 3.921A  pdb=" N   TRP A 293 " --> pdb=" O   GLY A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 332
      removed outlier: 3.521A  pdb=" N   VAL A 306 " --> pdb=" O   ASP A 302 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   LEU A 311 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 28
      removed outlier: 3.689A  pdb=" N   ARG B  28 " --> pdb=" O   HIS B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 48
    Processing helix  chain 'B' and resid 48 through 53
    Processing helix  chain 'B' and resid 89 through 127
      removed outlier: 3.549A  pdb=" N   ARG B  99 " --> pdb=" O   MET B  95 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLY B 127 " --> pdb=" O   ALA B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 142
    Processing helix  chain 'B' and resid 145 through 158
    Processing helix  chain 'B' and resid 160 through 189
      removed outlier: 3.832A  pdb=" N   PHE B 170 " --> pdb=" O   LEU B 166 " (cutoff:3.500A)
      Proline residue:  B 174  - end of helix
      removed outlier: 4.088A  pdb=" N   ASN B 189 " --> pdb=" O   LEU B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 199
      removed outlier: 3.604A  pdb=" N   THR B 194 " --> pdb=" O   ARG B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 210
    Processing helix  chain 'B' and resid 211 through 240
      removed outlier: 4.823A  pdb=" N   ALA B 217 " --> pdb=" O   PRO B 213 " (cutoff:3.500A)
      Proline residue:  B 218  - end of helix
      removed outlier: 3.966A  pdb=" N   VAL B 221 " --> pdb=" O   ALA B 217 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   GLN B 222 " --> pdb=" O   PRO B 218 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   SER B 224 " --> pdb=" O   ILE B 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 256
    Processing helix  chain 'B' and resid 260 through 265
      removed outlier: 4.680A  pdb=" N   SER B 264 " --> pdb=" O   GLN B 260 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 293
      removed outlier: 4.036A  pdb=" N   VAL B 269 " --> pdb=" O   ALA B 265 " (cutoff:3.500A)
      Proline residue:  B 272  - end of helix
    Processing helix  chain 'C' and resid 47 through 55
      removed outlier: 3.872A  pdb=" N   ILE C  53 " --> pdb=" O   SER C  49 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 87
    Processing helix  chain 'C' and resid 107 through 118
    Processing helix  chain 'C' and resid 123 through 138
    Processing helix  chain 'C' and resid 142 through 147
      removed outlier: 4.019A  pdb=" N   LEU C 147 " --> pdb=" O   PRO C 143 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 148 through 149
      No H-bonds generated for 'chain 'C' and resid 148 through 149'
    Processing helix  chain 'C' and resid 150 through 154
    Processing helix  chain 'C' and resid 155 through 169
    Processing helix  chain 'C' and resid 185 through 204
      removed outlier: 3.864A  pdb=" N   GLN C 191 " --> pdb=" O   THR C 187 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 213 through 221
      removed outlier: 3.855A  pdb=" N   VAL C 217 " --> pdb=" O   ASP C 213 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLU C 219 " --> pdb=" O   ALA C 215 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 239 through 243
      removed outlier: 3.685A  pdb=" N   PHE C 242 " --> pdb=" O   HIS C 239 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 247 through 256
    Processing helix  chain 'C' and resid 257 through 261
    Processing helix  chain 'C' and resid 294 through 300
      removed outlier: 3.881A  pdb=" N   ARG C 298 " --> pdb=" O   THR C 294 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 60 through 69
    Processing helix  chain 'D' and resid 90 through 100
      removed outlier: 3.526A  pdb=" N   ARG D  98 " --> pdb=" O   GLN D  94 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 117 through 130
      Proline residue:  D 125  - end of helix
    Processing helix  chain 'D' and resid 133 through 149
    Processing helix  chain 'D' and resid 151 through 155
    Processing helix  chain 'D' and resid 158 through 162
      removed outlier: 3.519A  pdb=" N   PHE D 162 " --> pdb=" O   PRO D 159 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 163 through 177
      removed outlier: 3.648A  pdb=" N   MET D 177 " --> pdb=" O   ALA D 173 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 193 through 212
    Processing helix  chain 'D' and resid 221 through 229
      removed outlier: 3.628A  pdb=" N   HIS D 227 " --> pdb=" O   SER D 223 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 246 through 252
    Processing helix  chain 'D' and resid 255 through 265
    Processing helix  chain 'D' and resid 303 through 308
      removed outlier: 3.896A  pdb=" N   THR D 307 " --> pdb=" O   GLY D 304 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 323 through 331
    Processing sheet with id=AA1, first strand: chain 'C' and resid 20 through 30
      removed outlier: 6.366A  pdb=" N   VAL C  11 " --> pdb=" O   ALA C  22 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   ASP C  24 " --> pdb=" O   LEU C   9 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   LEU C   9 " --> pdb=" O   ASP C  24 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   ILE C  26 " --> pdb=" O   ASP C   7 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   ASP C   7 " --> pdb=" O   ILE C  26 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   TYR C  28 " --> pdb=" O   ASN C   5 " (cutoff:3.500A)
      removed outlier: 4.677A  pdb=" N   ASN C   5 " --> pdb=" O   TYR C  28 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 20 through 30
      removed outlier: 6.366A  pdb=" N   VAL C  11 " --> pdb=" O   ALA C  22 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   ASP C  24 " --> pdb=" O   LEU C   9 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   LEU C   9 " --> pdb=" O   ASP C  24 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   ILE C  26 " --> pdb=" O   ASP C   7 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   ASP C   7 " --> pdb=" O   ILE C  26 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   TYR C  28 " --> pdb=" O   ASN C   5 " (cutoff:3.500A)
      removed outlier: 4.677A  pdb=" N   ASN C   5 " --> pdb=" O   TYR C  28 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 94
      removed outlier: 6.552A  pdb=" N   VAL C  35 " --> pdb=" O   LYS C 223 " (cutoff:3.500A)
      removed outlier: 7.941A  pdb=" N   ILE C 225 " --> pdb=" O   VAL C  35 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   GLY C  37 " --> pdb=" O   ILE C 225 " (cutoff:3.500A)
      removed outlier: 7.540A  pdb=" N   MET C 227 " --> pdb=" O   GLY C  37 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   VAL C  39 " --> pdb=" O   MET C 227 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   GLU C 234 " --> pdb=" O   VAL C 226 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   TYR C 228 " --> pdb=" O   VAL C 232 " (cutoff:3.500A)
      removed outlier: 5.208A  pdb=" N   VAL C 232 " --> pdb=" O   TYR C 228 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 32 through 45
      removed outlier: 6.502A  pdb=" N   LYS D  20 " --> pdb=" O   ALA D  37 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   ASP D  39 " --> pdb=" O   LEU D  18 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   LEU D  18 " --> pdb=" O   ASP D  39 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   VAL D  41 " --> pdb=" O   ILE D  16 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   ILE D  16 " --> pdb=" O   VAL D  41 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   PHE D  43 " --> pdb=" O   GLN D  14 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   GLN D  14 " --> pdb=" O   PHE D  43 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 101 through 104
      removed outlier: 6.613A  pdb=" N   GLN D 102 " --> pdb=" O   ILE D 184 " (cutoff:3.500A)
      removed outlier: 7.677A  pdb=" N   ASP D 186 " --> pdb=" O   GLN D 102 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   VAL D 104 " --> pdb=" O   ASP D 186 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   VAL D 183 " --> pdb=" O   VAL D 216 " (cutoff:3.500A)
      removed outlier: 7.550A  pdb=" N   ILE D 218 " --> pdb=" O   VAL D 183 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   ALA D 185 " --> pdb=" O   ILE D 218 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   THR D  50 " --> pdb=" O   GLU D 231 " (cutoff:3.500A)
      removed outlier: 7.875A  pdb=" N   MET D 233 " --> pdb=" O   THR D  50 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   ALA D  52 " --> pdb=" O   MET D 233 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   MET D 235 " --> pdb=" O   ALA D  52 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   VAL D  54 " --> pdb=" O   MET D 235 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   GLU D 242 " --> pdb=" O   VAL D 234 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   TYR D 236 " --> pdb=" O   CYS D 240 " (cutoff:3.500A)
      removed outlier: 5.419A  pdb=" N   CYS D 240 " --> pdb=" O   TYR D 236 " (cutoff:3.500A)

    526 hydrogen bonds defined for protein.
    1515 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.89

  Time building geometry restraints manager: 2.75 seconds

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

  Histogram of bond lengths:
        1.21 -     1.43: 4327
        1.43 -     1.64: 5300
        1.64 -     1.86: 117
        1.86 -     2.07: 0
        2.07 -     2.29: 24
  Bond restraints: 9768
  Sorted by residual:
  bond pdb=" CA  ALA B 217 "
       pdb=" CB  ALA B 217 "
    ideal  model  delta    sigma   weight residual
    1.534  1.426  0.108 1.18e-02 7.18e+03 8.35e+01
  bond pdb=" CE1 HIS D 227 "
       pdb=" NE2 HIS D 227 "
    ideal  model  delta    sigma   weight residual
    1.321  1.233  0.088 1.00e-02 1.00e+04 7.76e+01
  bond pdb=" CA  ALA D  52 "
       pdb=" CB  ALA D  52 "
    ideal  model  delta    sigma   weight residual
    1.529  1.419  0.110 1.34e-02 5.57e+03 6.74e+01
  bond pdb=" CE1 HIS A  68 "
       pdb=" NE2 HIS A  68 "
    ideal  model  delta    sigma   weight residual
    1.321  1.240  0.081 1.00e-02 1.00e+04 6.58e+01
  bond pdb=" CD2 HIS D 227 "
       pdb=" NE2 HIS D 227 "
    ideal  model  delta    sigma   weight residual
    1.374  1.285  0.089 1.10e-02 8.26e+03 6.54e+01
  ... (remaining 9763 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 9611
        2.16 -     4.32: 2941
        4.32 -     6.48: 513
        6.48 -     8.64: 193
        8.64 -    10.80: 23
  Bond angle restraints: 13281
  Sorted by residual:
  angle pdb=" C   HIS D 227 "
        pdb=" N   ILE D 228 "
        pdb=" CA  ILE D 228 "
      ideal   model   delta    sigma   weight residual
     122.66  129.78   -7.12 9.70e-01 1.06e+00 5.38e+01
  angle pdb=" CA  PHE D 217 "
        pdb=" CB  PHE D 217 "
        pdb=" CG  PHE D 217 "
      ideal   model   delta    sigma   weight residual
     113.80  120.88   -7.08 1.00e+00 1.00e+00 5.02e+01
  angle pdb=" CA  ASN C  85 "
        pdb=" CB  ASN C  85 "
        pdb=" CG  ASN C  85 "
      ideal   model   delta    sigma   weight residual
     112.60  119.64   -7.04 1.00e+00 1.00e+00 4.96e+01
  angle pdb=" CA  ASP C   7 "
        pdb=" CB  ASP C   7 "
        pdb=" CG  ASP C   7 "
      ideal   model   delta    sigma   weight residual
     112.60  119.55   -6.95 1.00e+00 1.00e+00 4.83e+01
  angle pdb=" CA  ASN D 202 "
        pdb=" CB  ASN D 202 "
        pdb=" CG  ASN D 202 "
      ideal   model   delta    sigma   weight residual
     112.60  119.52   -6.92 1.00e+00 1.00e+00 4.79e+01
  ... (remaining 13276 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.52: 5493
       17.52 -    35.03: 315
       35.03 -    52.54: 46
       52.54 -    70.06: 13
       70.06 -    87.57: 12
  Dihedral angle restraints: 5879
    sinusoidal: 2350
      harmonic: 3529
  Sorted by residual:
  dihedral pdb=" CA  ARG B  88 "
           pdb=" C   ARG B  88 "
           pdb=" N   ASP B  89 "
           pdb=" CA  ASP B  89 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.43  -28.57     0      5.00e+00 4.00e-02 3.26e+01
  dihedral pdb=" CA  ASP D 193 "
           pdb=" C   ASP D 193 "
           pdb=" N   VAL D 194 "
           pdb=" CA  VAL D 194 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.54  -25.46     0      5.00e+00 4.00e-02 2.59e+01
  dihedral pdb=" CA  GLN B 245 "
           pdb=" C   GLN B 245 "
           pdb=" N   PRO B 246 "
           pdb=" CA  PRO B 246 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.36  -24.64     0      5.00e+00 4.00e-02 2.43e+01
  ... (remaining 5876 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.145: 1121
       0.145 -    0.289: 153
       0.289 -    0.434: 49
       0.434 -    0.579: 152
       0.579 -    0.723: 66
  Chirality restraints: 1541
  Sorted by residual:
  chirality pdb=" CG  LEU B 285 "
            pdb=" CB  LEU B 285 "
            pdb=" CD1 LEU B 285 "
            pdb=" CD2 LEU B 285 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.87   -0.72 2.00e-01 2.50e+01 1.31e+01
  chirality pdb=" CG  LEU D 201 "
            pdb=" CB  LEU D 201 "
            pdb=" CD1 LEU D 201 "
            pdb=" CD2 LEU D 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.87   -0.72 2.00e-01 2.50e+01 1.29e+01
  chirality pdb=" CG  LEU D 313 "
            pdb=" CB  LEU D 313 "
            pdb=" CD1 LEU D 313 "
            pdb=" CD2 LEU D 313 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.87   -0.72 2.00e-01 2.50e+01 1.29e+01
  ... (remaining 1538 not shown)

  Planarity restraints: 1696
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 293 "    0.151 2.00e-02 2.50e+03   7.69e-02 1.48e+02
        pdb=" CG  TRP A 293 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 293 "   -0.043 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 293 "   -0.066 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 293 "   -0.051 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 293 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 293 "   -0.099 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 293 "    0.093 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 293 "   -0.038 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 293 "    0.081 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 251 "   -0.108 2.00e-02 2.50e+03   5.40e-02 7.29e+01
        pdb=" CG  TRP B 251 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 251 "    0.035 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 251 "    0.037 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 251 "    0.039 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 251 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 251 "    0.064 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 251 "   -0.074 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 251 "    0.033 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 251 "   -0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS C 316 "   -0.081 2.00e-02 2.50e+03   6.02e-02 5.43e+01
        pdb=" CG  HIS C 316 "    0.093 2.00e-02 2.50e+03
        pdb=" ND1 HIS C 316 "    0.033 2.00e-02 2.50e+03
        pdb=" CD2 HIS C 316 "    0.041 2.00e-02 2.50e+03
        pdb=" CE1 HIS C 316 "   -0.037 2.00e-02 2.50e+03
        pdb=" NE2 HIS C 316 "   -0.049 2.00e-02 2.50e+03
  ... (remaining 1693 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1769
        2.81 -     3.33: 9426
        3.33 -     3.86: 15116
        3.86 -     4.38: 17325
        4.38 -     4.90: 30386
  Nonbonded interactions: 74022
  Sorted by model distance:
  nonbonded pdb=" OG  SER D 133 "
            pdb=" OE2 GLU D 135 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" N   GLN D 312 "
            pdb=" OE1 GLN D 312 "
     model   vdw
     2.387 3.120
  nonbonded pdb=" OE2 GLU D 123 "
            pdb=" OH  TYR D 155 "
     model   vdw
     2.523 3.040
  nonbonded pdb=" OE2 GLU B 187 "
            pdb=" OH  TYR B 192 "
     model   vdw
     2.536 3.040
  nonbonded pdb=" OE1 GLU C  80 "
            pdb=" NH1 ARG C  84 "
     model   vdw
     2.542 3.120
  ... (remaining 74017 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.160
  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:          0.290
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     25.820
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.040
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6971
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      :  0.025   0.139   9768  Z= 1.690
  Angle     :  2.211  10.795  13281  Z= 1.488
  Chirality :  0.239   0.723   1541
  Planarity :  0.014   0.128   1696
  Dihedral  : 12.466  87.571   3611
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 0.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  7.41 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.22), residues: 1224
  helix: -0.76 (0.17), residues: 665
  sheet: -0.44 (0.49), residues: 91
  loop : -0.14 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.151   0.018   TRP A 293 
 HIS   0.016   0.003   HIS C 247 
 PHE   0.080   0.012   PHE D 162 
 TYR   0.089   0.016   TYR D  81 
 ARG   0.009   0.001   ARG C  62 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  365 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 365
  time to evaluate  : 1.094 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 PHE cc_start: 0.7210 (t80) cc_final: 0.6996 (t80)
REVERT: A   62 MET cc_start: 0.6855 (mtm) cc_final: 0.6506 (mtm)
REVERT: A  151 MET cc_start: 0.7339 (mmm) cc_final: 0.7043 (mmm)
REVERT: A  175 LEU cc_start: 0.8916 (mt) cc_final: 0.8702 (mp)
REVERT: A  222 ARG cc_start: 0.7206 (mtp85) cc_final: 0.6916 (mtp85)
REVERT: A  247 ARG cc_start: 0.7411 (ttp80) cc_final: 0.6849 (ttp80)
REVERT: A  296 ASP cc_start: 0.7424 (t0) cc_final: 0.7069 (t0)
REVERT: A  300 ARG cc_start: 0.7927 (ttm-80) cc_final: 0.7648 (ttm-80)
REVERT: B   60 GLN cc_start: 0.8488 (mt0) cc_final: 0.7562 (mt0)
REVERT: B   61 PHE cc_start: 0.7161 (m-80) cc_final: 0.6771 (m-80)
REVERT: B   62 ARG cc_start: 0.7170 (ptp90) cc_final: 0.6424 (ptp90)
REVERT: B   77 MET cc_start: 0.8014 (tpp) cc_final: 0.7643 (tpp)
REVERT: B   84 ASP cc_start: 0.7280 (t0) cc_final: 0.6857 (t0)
REVERT: B  115 MET cc_start: 0.6860 (mtp) cc_final: 0.6515 (mtp)
REVERT: B  210 ASN cc_start: 0.8179 (m-40) cc_final: 0.7928 (m-40)
REVERT: B  254 MET cc_start: 0.8177 (mtp) cc_final: 0.7914 (mtm)
REVERT: C   15 ASP cc_start: 0.6594 (t70) cc_final: 0.6264 (t70)
REVERT: C   41 GLU cc_start: 0.7048 (pt0) cc_final: 0.6641 (pt0)
REVERT: C   50 SER cc_start: 0.7203 (m) cc_final: 0.6755 (p)
REVERT: C   95 PHE cc_start: 0.8608 (m-80) cc_final: 0.8401 (m-80)
REVERT: C  124 LYS cc_start: 0.7470 (tppp) cc_final: 0.7127 (tppp)
REVERT: C  142 ASP cc_start: 0.7243 (t0) cc_final: 0.6496 (t0)
REVERT: C  149 VAL cc_start: 0.7559 (t) cc_final: 0.7206 (p)
REVERT: C  158 MET cc_start: 0.7492 (mmm) cc_final: 0.6965 (mmm)
REVERT: C  168 ILE cc_start: 0.7800 (tp) cc_final: 0.7503 (tp)
REVERT: C  173 LYS cc_start: 0.7455 (ttmt) cc_final: 0.7046 (ttmm)
REVERT: C  198 GLU cc_start: 0.7474 (tp30) cc_final: 0.7242 (tp30)
REVERT: C  202 LYS cc_start: 0.7898 (ttpp) cc_final: 0.7665 (ttpp)
REVERT: C  213 ASP cc_start: 0.7651 (t0) cc_final: 0.7152 (t0)
REVERT: C  259 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7602 (mt-10)
REVERT: C  319 LEU cc_start: 0.8015 (mp) cc_final: 0.7758 (mt)
REVERT: D   28 MET cc_start: 0.7147 (tmm) cc_final: 0.6879 (tmm)
REVERT: D   33 ARG cc_start: 0.7193 (mtm110) cc_final: 0.6950 (mtm110)
REVERT: D   36 LYS cc_start: 0.7882 (mttt) cc_final: 0.7427 (mttp)
REVERT: D   39 ASP cc_start: 0.7271 (t0) cc_final: 0.6639 (t0)
REVERT: D   72 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7246 (mt-10)
REVERT: D   84 GLN cc_start: 0.7234 (tt0) cc_final: 0.6855 (tt0)
REVERT: D  117 LYS cc_start: 0.7179 (mttt) cc_final: 0.6816 (mttp)
REVERT: D  131 SER cc_start: 0.8437 (m) cc_final: 0.8142 (t)
REVERT: D  151 LYS cc_start: 0.7496 (mttp) cc_final: 0.7182 (mtmm)
REVERT: D  179 ASP cc_start: 0.7820 (t0) cc_final: 0.7508 (t0)
REVERT: D  210 GLU cc_start: 0.7528 (tt0) cc_final: 0.7288 (tt0)
REVERT: D  221 ASP cc_start: 0.7057 (t0) cc_final: 0.6678 (t0)
REVERT: D  226 GLU cc_start: 0.7985 (tt0) cc_final: 0.7558 (tt0)
REVERT: D  271 ASP cc_start: 0.7058 (t70) cc_final: 0.6643 (t0)
REVERT: D  312 GLN cc_start: 0.7641 (pm20) cc_final: 0.7402 (pm20)
REVERT: D  314 LYS cc_start: 0.7097 (ttmm) cc_final: 0.6885 (ttmm)
REVERT: D  327 ASP cc_start: 0.7454 (t70) cc_final: 0.7206 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 365
  average time/residue: 0.2829
  time to fit residues: 132.6082
Evaluate side-chains
  320 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 320
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 62 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9990
   chunk 95 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 58 optimal weight:    0.6980
   chunk 71 optimal weight:    0.5980
   chunk 110 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B  24 HIS
C 120 GLN
C 160 GLN
D 208 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.114341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.103124 restraints weight = 13700.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 1.94
r_work: 0.3199 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3051 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9768  Z= 0.254
  Angle     :  0.625   7.049  13281  Z= 0.331
  Chirality :  0.046   0.185   1541
  Planarity :  0.005   0.047   1696
  Dihedral  :  5.152  24.757   1336
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  8.98 %
    Favored  : 89.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.24), residues: 1224
  helix:  1.18 (0.20), residues: 663
  sheet: -0.20 (0.53), residues: 94
  loop : -0.11 (0.30), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 293 
 HIS   0.005   0.001   HIS C 247 
 PHE   0.017   0.002   PHE D 303 
 TYR   0.013   0.001   TYR A 236 
 ARG   0.007   0.001   ARG D 276 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  355 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 336
  time to evaluate  : 1.010 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 PHE cc_start: 0.8438 (t80) cc_final: 0.8110 (t80)
REVERT: A   62 MET cc_start: 0.6858 (mtm) cc_final: 0.6590 (mtm)
REVERT: A   96 PHE cc_start: 0.8540 (t80) cc_final: 0.7825 (t80)
REVERT: A  151 MET cc_start: 0.8649 (mmm) cc_final: 0.8417 (mmp)
REVERT: A  156 VAL cc_start: 0.8317 (t) cc_final: 0.8062 (m)
REVERT: A  185 MET cc_start: 0.7865 (tpp) cc_final: 0.7590 (tpp)
REVERT: A  219 VAL cc_start: 0.8701 (t) cc_final: 0.8388 (p)
REVERT: A  247 ARG cc_start: 0.8319 (ttp80) cc_final: 0.7952 (ttp80)
REVERT: A  300 ARG cc_start: 0.8531 (ttm-80) cc_final: 0.8031 (ttm-80)
REVERT: A  336 ARG cc_start: 0.7569 (mtm180) cc_final: 0.5907 (mmm160)
REVERT: B   47 ILE cc_start: 0.8487 (tp) cc_final: 0.8232 (tp)
REVERT: B   84 ASP cc_start: 0.8081 (t0) cc_final: 0.7860 (t0)
REVERT: B  126 PHE cc_start: 0.8804 (m-80) cc_final: 0.8493 (m-80)
REVERT: B  140 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8367 (mt)
REVERT: B  185 LEU cc_start: 0.8563 (mt) cc_final: 0.8345 (mm)
REVERT: B  204 MET cc_start: 0.8041 (ppp) cc_final: 0.7835 (ppp)
REVERT: B  212 PHE cc_start: 0.8416 (t80) cc_final: 0.8214 (t80)
REVERT: B  248 THR cc_start: 0.9146 (t) cc_final: 0.8936 (p)
REVERT: B  286 MET cc_start: 0.7606 (mmp) cc_final: 0.7005 (mmm)
REVERT: C   15 ASP cc_start: 0.7754 (t70) cc_final: 0.7432 (t70)
REVERT: C   25 ARG cc_start: 0.8292 (mtm-85) cc_final: 0.8070 (mtm-85)
REVERT: C   41 GLU cc_start: 0.7468 (pt0) cc_final: 0.7124 (pt0)
REVERT: C   50 SER cc_start: 0.8324 (m) cc_final: 0.7876 (p)
REVERT: C   80 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6716 (tm-30)
REVERT: C  149 VAL cc_start: 0.8471 (t) cc_final: 0.8203 (p)
REVERT: C  168 ILE cc_start: 0.8526 (tp) cc_final: 0.8291 (tp)
REVERT: C  173 LYS cc_start: 0.8381 (ttmt) cc_final: 0.8147 (ttmm)
REVERT: C  198 GLU cc_start: 0.8093 (tp30) cc_final: 0.7845 (tp30)
REVERT: C  200 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8329 (tm-30)
REVERT: C  213 ASP cc_start: 0.7806 (t0) cc_final: 0.7361 (t0)
REVERT: C  234 GLU cc_start: 0.7936 (tt0) cc_final: 0.7556 (tt0)
REVERT: D   28 MET cc_start: 0.6996 (tmm) cc_final: 0.6585 (tmm)
REVERT: D   36 LYS cc_start: 0.8409 (mttt) cc_final: 0.8123 (mtmp)
REVERT: D   39 ASP cc_start: 0.7739 (t0) cc_final: 0.6915 (t0)
REVERT: D   54 VAL cc_start: 0.8451 (m) cc_final: 0.8181 (p)
REVERT: D   92 GLN cc_start: 0.7465 (pm20) cc_final: 0.7128 (pm20)
REVERT: D  116 LYS cc_start: 0.8896 (mmmt) cc_final: 0.8652 (mmtm)
REVERT: D  140 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7973 (ttmm)
REVERT: D  144 MET cc_start: 0.8032 (tpp) cc_final: 0.7613 (mpp)
REVERT: D  179 ASP cc_start: 0.8193 (t0) cc_final: 0.7942 (t0)
REVERT: D  205 MET cc_start: 0.8103 (mmp) cc_final: 0.7863 (mmp)
REVERT: D  210 GLU cc_start: 0.8190 (tt0) cc_final: 0.7961 (tt0)
REVERT: D  226 GLU cc_start: 0.8167 (tt0) cc_final: 0.7835 (tt0)
REVERT: D  252 ASN cc_start: 0.8881 (t0) cc_final: 0.8393 (t0)
REVERT: D  271 ASP cc_start: 0.7491 (t70) cc_final: 0.6961 (t0)
REVERT: D  309 LEU cc_start: 0.8218 (mt) cc_final: 0.7994 (mm)
REVERT: D  314 LYS cc_start: 0.8362 (ttmm) cc_final: 0.8088 (ttmm)
REVERT: D  327 ASP cc_start: 0.8431 (t70) cc_final: 0.8039 (t0)
  outliers start: 19
  outliers final: 10
  residues processed: 342
  average time/residue: 0.2967
  time to fit residues: 129.6654
Evaluate side-chains
  316 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 304
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  246 THR
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain B residue  227 PHE
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  199 LEU
Chi-restraints excluded: chain C residue  274 VAL
Chi-restraints excluded: chain D residue   42 SER
Chi-restraints excluded: chain D residue  140 LYS
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain D residue  237 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 105 optimal weight:    0.9980
   chunk 112 optimal weight:    1.9990
   chunk 94 optimal weight:    0.6980
   chunk 5 optimal weight:    0.2980
   chunk 16 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 108 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 117 optimal weight:    3.9990
   chunk 114 optimal weight:    0.0870
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
B  60 GLN
C 316 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.114543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.103255 restraints weight = 13863.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 1.97
r_work: 0.3201 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9768  Z= 0.217
  Angle     :  0.548   5.949  13281  Z= 0.282
  Chirality :  0.043   0.173   1541
  Planarity :  0.005   0.036   1696
  Dihedral  :  4.557  19.491   1336
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.66 %
    Favored  : 84.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.24), residues: 1224
  helix:  1.67 (0.20), residues: 666
  sheet: -0.09 (0.55), residues: 94
  loop : -0.27 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 293 
 HIS   0.003   0.001   HIS A 254 
 PHE   0.014   0.001   PHE D 303 
 TYR   0.010   0.001   TYR A 236 
 ARG   0.006   0.001   ARG A 249 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  337 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 317
  time to evaluate  : 1.051 
Fit side-chains
REVERT: A   62 MET cc_start: 0.6774 (mtm) cc_final: 0.6528 (mtm)
REVERT: A   74 MET cc_start: 0.7640 (ppp) cc_final: 0.7149 (ppp)
REVERT: A   96 PHE cc_start: 0.8568 (t80) cc_final: 0.7836 (t80)
REVERT: A  151 MET cc_start: 0.8664 (mmm) cc_final: 0.8379 (mmp)
REVERT: A  156 VAL cc_start: 0.8311 (t) cc_final: 0.8031 (m)
REVERT: A  172 MET cc_start: 0.8668 (ppp) cc_final: 0.8180 (ppp)
REVERT: A  173 VAL cc_start: 0.8900 (t) cc_final: 0.8673 (p)
REVERT: A  185 MET cc_start: 0.7859 (tpp) cc_final: 0.7557 (tpp)
REVERT: A  247 ARG cc_start: 0.8317 (ttp80) cc_final: 0.7984 (ttp80)
REVERT: A  300 ARG cc_start: 0.8491 (ttm-80) cc_final: 0.8076 (mtm-85)
REVERT: B   47 ILE cc_start: 0.8530 (tp) cc_final: 0.8287 (tp)
REVERT: B  126 PHE cc_start: 0.8756 (m-80) cc_final: 0.8542 (m-80)
REVERT: B  196 SER cc_start: 0.8760 (m) cc_final: 0.8539 (t)
REVERT: B  204 MET cc_start: 0.7991 (ppp) cc_final: 0.7760 (ppp)
REVERT: B  227 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7771 (t80)
REVERT: B  286 MET cc_start: 0.7778 (mmp) cc_final: 0.7522 (mmm)
REVERT: C   15 ASP cc_start: 0.7913 (t70) cc_final: 0.7656 (t70)
REVERT: C   16 GLU cc_start: 0.7988 (tp30) cc_final: 0.7721 (tp30)
REVERT: C   24 ASP cc_start: 0.8117 (t0) cc_final: 0.7690 (t0)
REVERT: C   25 ARG cc_start: 0.8310 (mtm-85) cc_final: 0.8075 (mtm-85)
REVERT: C   41 GLU cc_start: 0.7399 (pt0) cc_final: 0.7086 (pt0)
REVERT: C   50 SER cc_start: 0.8344 (m) cc_final: 0.7921 (p)
REVERT: C   82 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7367 (mm-30)
REVERT: C  149 VAL cc_start: 0.8439 (t) cc_final: 0.8077 (p)
REVERT: C  168 ILE cc_start: 0.8555 (tp) cc_final: 0.8353 (tp)
REVERT: C  171 ARG cc_start: 0.8253 (mmt180) cc_final: 0.7820 (mmt90)
REVERT: C  173 LYS cc_start: 0.8314 (ttmt) cc_final: 0.8071 (ttmm)
REVERT: C  198 GLU cc_start: 0.8052 (tp30) cc_final: 0.7797 (tp30)
REVERT: C  213 ASP cc_start: 0.7829 (t0) cc_final: 0.7390 (t0)
REVERT: C  234 GLU cc_start: 0.7981 (tt0) cc_final: 0.7613 (tt0)
REVERT: C  259 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7732 (mt-10)
REVERT: D   28 MET cc_start: 0.7031 (tmm) cc_final: 0.6678 (tmm)
REVERT: D   36 LYS cc_start: 0.8416 (mttt) cc_final: 0.8079 (mttp)
REVERT: D   39 ASP cc_start: 0.7758 (t0) cc_final: 0.6973 (t0)
REVERT: D   92 GLN cc_start: 0.7378 (pm20) cc_final: 0.7048 (pm20)
REVERT: D  116 LYS cc_start: 0.8808 (mmmt) cc_final: 0.8586 (mmtm)
REVERT: D  144 MET cc_start: 0.8057 (tpp) cc_final: 0.7628 (mpp)
REVERT: D  177 MET cc_start: 0.8317 (mmm) cc_final: 0.7838 (mmm)
REVERT: D  210 GLU cc_start: 0.8158 (tt0) cc_final: 0.7920 (tt0)
REVERT: D  226 GLU cc_start: 0.8182 (tt0) cc_final: 0.7943 (tt0)
REVERT: D  252 ASN cc_start: 0.8942 (t0) cc_final: 0.8569 (t0)
REVERT: D  267 ARG cc_start: 0.7955 (mmm160) cc_final: 0.7693 (ttm-80)
REVERT: D  276 ARG cc_start: 0.6518 (ttm110) cc_final: 0.6276 (ttm110)
REVERT: D  309 LEU cc_start: 0.8249 (mt) cc_final: 0.8045 (mp)
REVERT: D  314 LYS cc_start: 0.8321 (ttmm) cc_final: 0.8077 (ttmm)
  outliers start: 20
  outliers final: 14
  residues processed: 326
  average time/residue: 0.2961
  time to fit residues: 123.5904
Evaluate side-chains
  315 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 300
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  227 PHE
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  199 LEU
Chi-restraints excluded: chain C residue  274 VAL
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue  128 ILE
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain D residue  237 LEU
Chi-restraints excluded: chain D residue  329 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 117 optimal weight:    0.2980
   chunk 79 optimal weight:    0.0770
   chunk 27 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0060
   chunk 76 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 85 optimal weight:    2.9990
   overall best weight:    0.3954

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

Flipped N/Q/H residues before XYZ refinement:
B  60 GLN
** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.115060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.103773 restraints weight = 13738.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 1.95
r_work: 0.3205 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.2664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9768  Z= 0.181
  Angle     :  0.527   8.348  13281  Z= 0.267
  Chirality :  0.041   0.169   1541
  Planarity :  0.004   0.042   1696
  Dihedral  :  4.311  18.747   1336
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 15.90 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.25), residues: 1224
  helix:  1.85 (0.20), residues: 668
  sheet: -0.11 (0.55), residues: 94
  loop : -0.34 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 293 
 HIS   0.005   0.001   HIS C  12 
 PHE   0.013   0.001   PHE D 303 
 TYR   0.010   0.001   TYR A 236 
 ARG   0.008   0.000   ARG A 249 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  335 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 312
  time to evaluate  : 1.092 
Fit side-chains
REVERT: A   62 MET cc_start: 0.6787 (mtm) cc_final: 0.6534 (mtm)
REVERT: A   74 MET cc_start: 0.7633 (ppp) cc_final: 0.7105 (ppp)
REVERT: A   96 PHE cc_start: 0.8563 (t80) cc_final: 0.7808 (t80)
REVERT: A  134 VAL cc_start: 0.8285 (t) cc_final: 0.8071 (p)
REVERT: A  151 MET cc_start: 0.8660 (mmm) cc_final: 0.8351 (mmp)
REVERT: A  156 VAL cc_start: 0.8292 (t) cc_final: 0.8027 (m)
REVERT: A  172 MET cc_start: 0.8676 (ppp) cc_final: 0.8315 (ppp)
REVERT: A  173 VAL cc_start: 0.8924 (t) cc_final: 0.8715 (p)
REVERT: A  185 MET cc_start: 0.7879 (tpp) cc_final: 0.7588 (tpp)
REVERT: A  247 ARG cc_start: 0.8295 (ttp80) cc_final: 0.7958 (ttp80)
REVERT: A  300 ARG cc_start: 0.8455 (ttm-80) cc_final: 0.8104 (mtm-85)
REVERT: B   47 ILE cc_start: 0.8536 (tp) cc_final: 0.8307 (tp)
REVERT: B  204 MET cc_start: 0.7972 (ppp) cc_final: 0.7737 (ppp)
REVERT: B  227 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7829 (t80)
REVERT: B  286 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7362 (mmm)
REVERT: C   15 ASP cc_start: 0.7925 (t70) cc_final: 0.7693 (t70)
REVERT: C   16 GLU cc_start: 0.7926 (tp30) cc_final: 0.7682 (tp30)
REVERT: C   24 ASP cc_start: 0.8088 (t0) cc_final: 0.7680 (t0)
REVERT: C   50 SER cc_start: 0.8346 (m) cc_final: 0.7941 (p)
REVERT: C   82 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7371 (mm-30)
REVERT: C  138 VAL cc_start: 0.8448 (m) cc_final: 0.8159 (t)
REVERT: C  149 VAL cc_start: 0.8451 (t) cc_final: 0.8067 (p)
REVERT: C  168 ILE cc_start: 0.8640 (tp) cc_final: 0.8298 (pt)
REVERT: C  171 ARG cc_start: 0.8272 (mmt180) cc_final: 0.7797 (mmt90)
REVERT: C  198 GLU cc_start: 0.8072 (tp30) cc_final: 0.7814 (tp30)
REVERT: C  201 GLN cc_start: 0.8650 (mm-40) cc_final: 0.8344 (mm-40)
REVERT: C  213 ASP cc_start: 0.7850 (t0) cc_final: 0.7430 (t0)
REVERT: C  234 GLU cc_start: 0.7964 (tt0) cc_final: 0.7587 (tt0)
REVERT: C  259 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7749 (mt-10)
REVERT: C  296 ARG cc_start: 0.8608 (ttp-170) cc_final: 0.8376 (ttp80)
REVERT: C  320 ASP cc_start: 0.8395 (p0) cc_final: 0.7899 (p0)
REVERT: D   28 MET cc_start: 0.7008 (tmm) cc_final: 0.6698 (tmm)
REVERT: D   36 LYS cc_start: 0.8431 (mttt) cc_final: 0.8103 (mttp)
REVERT: D   84 GLN cc_start: 0.8194 (tt0) cc_final: 0.7967 (mt0)
REVERT: D   92 GLN cc_start: 0.7448 (pm20) cc_final: 0.7113 (pm20)
REVERT: D  116 LYS cc_start: 0.8804 (mmmt) cc_final: 0.8570 (mmtm)
REVERT: D  137 ARG cc_start: 0.8362 (mtm-85) cc_final: 0.8150 (mtm-85)
REVERT: D  144 MET cc_start: 0.8081 (tpp) cc_final: 0.7638 (mpp)
REVERT: D  177 MET cc_start: 0.8326 (mmm) cc_final: 0.7888 (mmm)
REVERT: D  210 GLU cc_start: 0.8173 (tt0) cc_final: 0.7938 (tt0)
REVERT: D  226 GLU cc_start: 0.8163 (tt0) cc_final: 0.7927 (tt0)
REVERT: D  252 ASN cc_start: 0.8943 (t0) cc_final: 0.8546 (t0)
REVERT: D  267 ARG cc_start: 0.7987 (mmm160) cc_final: 0.7728 (ttm-80)
  outliers start: 23
  outliers final: 17
  residues processed: 318
  average time/residue: 0.2955
  time to fit residues: 119.7826
Evaluate side-chains
  323 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 304
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  246 THR
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  227 PHE
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain B residue  286 MET
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  199 LEU
Chi-restraints excluded: chain C residue  274 VAL
Chi-restraints excluded: chain C residue  319 LEU
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue   70 MET
Chi-restraints excluded: chain D residue   78 GLU
Chi-restraints excluded: chain D residue   95 LYS
Chi-restraints excluded: chain D residue  128 ILE
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain D residue  233 MET
Chi-restraints excluded: chain D residue  237 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   chunk 103 optimal weight:    0.6980
   chunk 99 optimal weight:    0.0970
   chunk 117 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 26 optimal weight:    0.3980
   chunk 47 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.113984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.102151 restraints weight = 13813.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 2.15
r_work: 0.3178 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3022 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.2817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9768  Z= 0.223
  Angle     :  0.537   9.016  13281  Z= 0.270
  Chirality :  0.042   0.158   1541
  Planarity :  0.004   0.041   1696
  Dihedral  :  4.201  18.650   1336
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 16.78 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.25), residues: 1224
  helix:  1.93 (0.20), residues: 668
  sheet: -0.10 (0.57), residues: 94
  loop : -0.36 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 293 
 HIS   0.004   0.001   HIS C  12 
 PHE   0.013   0.001   PHE C  70 
 TYR   0.010   0.001   TYR A 236 
 ARG   0.010   0.000   ARG A 249 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  339 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 310
  time to evaluate  : 0.988 
Fit side-chains
REVERT: A   24 PHE cc_start: 0.8466 (t80) cc_final: 0.8211 (t80)
REVERT: A   62 MET cc_start: 0.6806 (mtm) cc_final: 0.6542 (mtm)
REVERT: A   74 MET cc_start: 0.7704 (ppp) cc_final: 0.7175 (ppp)
REVERT: A   96 PHE cc_start: 0.8566 (t80) cc_final: 0.7829 (t80)
REVERT: A  151 MET cc_start: 0.8612 (mmm) cc_final: 0.8281 (mmp)
REVERT: A  156 VAL cc_start: 0.8383 (t) cc_final: 0.8085 (m)
REVERT: A  172 MET cc_start: 0.8705 (ppp) cc_final: 0.8119 (ppp)
REVERT: A  185 MET cc_start: 0.7964 (tpp) cc_final: 0.7653 (tpp)
REVERT: A  247 ARG cc_start: 0.8403 (ttp80) cc_final: 0.8079 (ttp80)
REVERT: A  300 ARG cc_start: 0.8496 (ttm-80) cc_final: 0.8111 (mtm-85)
REVERT: B   47 ILE cc_start: 0.8601 (tp) cc_final: 0.8386 (tp)
REVERT: B  204 MET cc_start: 0.8037 (ppp) cc_final: 0.7801 (ppp)
REVERT: B  227 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7841 (t80)
REVERT: B  286 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7668 (mmm)
REVERT: C   16 GLU cc_start: 0.7943 (tp30) cc_final: 0.7730 (tp30)
REVERT: C   24 ASP cc_start: 0.8101 (t0) cc_final: 0.7718 (t0)
REVERT: C   50 SER cc_start: 0.8371 (m) cc_final: 0.8019 (p)
REVERT: C   70 PHE cc_start: 0.8593 (t80) cc_final: 0.8350 (t80)
REVERT: C   82 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7438 (mm-30)
REVERT: C  138 VAL cc_start: 0.8479 (m) cc_final: 0.8199 (t)
REVERT: C  149 VAL cc_start: 0.8470 (t) cc_final: 0.8112 (p)
REVERT: C  168 ILE cc_start: 0.8707 (tp) cc_final: 0.8394 (pt)
REVERT: C  171 ARG cc_start: 0.8277 (mmt180) cc_final: 0.7859 (mmt90)
REVERT: C  173 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8070 (mtpp)
REVERT: C  198 GLU cc_start: 0.8180 (tp30) cc_final: 0.7838 (tp30)
REVERT: C  201 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8397 (mm-40)
REVERT: C  213 ASP cc_start: 0.7880 (t0) cc_final: 0.7481 (t0)
REVERT: C  234 GLU cc_start: 0.7996 (tt0) cc_final: 0.7427 (tt0)
REVERT: C  296 ARG cc_start: 0.8666 (ttp-170) cc_final: 0.8410 (ttp80)
REVERT: C  314 LYS cc_start: 0.8742 (ttmt) cc_final: 0.8512 (tttt)
REVERT: D   28 MET cc_start: 0.7089 (tmm) cc_final: 0.6783 (tmm)
REVERT: D   36 LYS cc_start: 0.8415 (mttt) cc_final: 0.8143 (mtmp)
REVERT: D   67 LEU cc_start: 0.8266 (mt) cc_final: 0.7891 (mp)
REVERT: D   84 GLN cc_start: 0.8318 (tt0) cc_final: 0.8099 (mt0)
REVERT: D   92 GLN cc_start: 0.7494 (pm20) cc_final: 0.7168 (pm20)
REVERT: D  116 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8567 (mmtm)
REVERT: D  137 ARG cc_start: 0.8433 (mtm-85) cc_final: 0.8214 (mtm-85)
REVERT: D  144 MET cc_start: 0.8164 (tpp) cc_final: 0.7721 (mpp)
REVERT: D  192 LEU cc_start: 0.8729 (mt) cc_final: 0.8471 (mp)
REVERT: D  210 GLU cc_start: 0.8206 (tt0) cc_final: 0.7979 (tt0)
REVERT: D  226 GLU cc_start: 0.8229 (tt0) cc_final: 0.8014 (tt0)
REVERT: D  252 ASN cc_start: 0.8963 (t0) cc_final: 0.8666 (t0)
REVERT: D  267 ARG cc_start: 0.8069 (mmm160) cc_final: 0.7809 (ttm-80)
  outliers start: 29
  outliers final: 20
  residues processed: 319
  average time/residue: 0.2955
  time to fit residues: 120.5005
Evaluate side-chains
  326 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 303
  time to evaluate  : 1.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  246 THR
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue   76 SER
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  141 MET
Chi-restraints excluded: chain B residue  227 PHE
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain B residue  286 MET
Chi-restraints excluded: chain C residue  173 LYS
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  199 LEU
Chi-restraints excluded: chain C residue  274 VAL
Chi-restraints excluded: chain C residue  319 LEU
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue   78 GLU
Chi-restraints excluded: chain D residue   95 LYS
Chi-restraints excluded: chain D residue  128 ILE
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain D residue  233 MET
Chi-restraints excluded: chain D residue  237 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 68 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 88 optimal weight:    0.0170
   chunk 87 optimal weight:    0.9980
   chunk 115 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9980
   chunk 94 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.6818

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

Flipped N/Q/H residues before XYZ refinement:
C 247 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.113409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.101594 restraints weight = 13769.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 2.14
r_work: 0.3166 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9768  Z= 0.254
  Angle     :  0.550   7.847  13281  Z= 0.276
  Chirality :  0.043   0.158   1541
  Planarity :  0.004   0.043   1696
  Dihedral  :  4.204  18.881   1336
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 18.34 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.25), residues: 1224
  helix:  1.98 (0.20), residues: 668
  sheet: -0.22 (0.56), residues: 94
  loop : -0.46 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 293 
 HIS   0.005   0.001   HIS C  12 
 PHE   0.013   0.001   PHE D 303 
 TYR   0.010   0.001   TYR A 236 
 ARG   0.010   0.001   ARG A 249 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 304
  time to evaluate  : 1.039 
Fit side-chains
REVERT: A   24 PHE cc_start: 0.8463 (t80) cc_final: 0.8230 (t80)
REVERT: A   62 MET cc_start: 0.6809 (mtm) cc_final: 0.6546 (mtm)
REVERT: A   74 MET cc_start: 0.7678 (ppp) cc_final: 0.7120 (ppp)
REVERT: A   96 PHE cc_start: 0.8589 (t80) cc_final: 0.7854 (t80)
REVERT: A  151 MET cc_start: 0.8564 (mmm) cc_final: 0.8244 (mmp)
REVERT: A  172 MET cc_start: 0.8613 (ppp) cc_final: 0.7992 (ppp)
REVERT: A  185 MET cc_start: 0.7954 (tpp) cc_final: 0.7670 (tpp)
REVERT: A  247 ARG cc_start: 0.8381 (ttp80) cc_final: 0.8057 (ttp80)
REVERT: A  300 ARG cc_start: 0.8480 (ttm-80) cc_final: 0.8038 (mtm-85)
REVERT: B  204 MET cc_start: 0.8036 (ppp) cc_final: 0.7795 (ppp)
REVERT: B  227 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7877 (t80)
REVERT: C   16 GLU cc_start: 0.7969 (tp30) cc_final: 0.7668 (tp30)
REVERT: C   24 ASP cc_start: 0.8136 (t0) cc_final: 0.7749 (t0)
REVERT: C   50 SER cc_start: 0.8341 (m) cc_final: 0.7989 (p)
REVERT: C   82 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7473 (mm-30)
REVERT: C  138 VAL cc_start: 0.8490 (m) cc_final: 0.8194 (t)
REVERT: C  149 VAL cc_start: 0.8479 (t) cc_final: 0.8116 (p)
REVERT: C  168 ILE cc_start: 0.8699 (tp) cc_final: 0.8385 (pt)
REVERT: C  171 ARG cc_start: 0.8260 (mmt180) cc_final: 0.7829 (mmt90)
REVERT: C  173 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8076 (mtpp)
REVERT: C  198 GLU cc_start: 0.8183 (tp30) cc_final: 0.7832 (tp30)
REVERT: C  201 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8406 (mm-40)
REVERT: C  213 ASP cc_start: 0.7869 (t0) cc_final: 0.7474 (t0)
REVERT: C  234 GLU cc_start: 0.7972 (tt0) cc_final: 0.7406 (tt0)
REVERT: C  320 ASP cc_start: 0.8508 (p0) cc_final: 0.7963 (p0)
REVERT: D   28 MET cc_start: 0.7121 (tmm) cc_final: 0.6798 (tmm)
REVERT: D   36 LYS cc_start: 0.8415 (mttt) cc_final: 0.8137 (mtmp)
REVERT: D   84 GLN cc_start: 0.8309 (tt0) cc_final: 0.8084 (mt0)
REVERT: D   92 GLN cc_start: 0.7491 (pm20) cc_final: 0.7186 (pm20)
REVERT: D  116 LYS cc_start: 0.8799 (mmmt) cc_final: 0.8534 (mmtm)
REVERT: D  137 ARG cc_start: 0.8419 (mtm-85) cc_final: 0.8138 (mtm180)
REVERT: D  144 MET cc_start: 0.8180 (tpp) cc_final: 0.7743 (mpp)
REVERT: D  192 LEU cc_start: 0.8759 (mt) cc_final: 0.8512 (mp)
REVERT: D  210 GLU cc_start: 0.8189 (tt0) cc_final: 0.7975 (tt0)
REVERT: D  226 GLU cc_start: 0.8202 (tt0) cc_final: 0.7987 (tt0)
REVERT: D  252 ASN cc_start: 0.8939 (t0) cc_final: 0.8632 (t0)
REVERT: D  267 ARG cc_start: 0.7976 (mmm160) cc_final: 0.7774 (ttm-80)
  outliers start: 22
  outliers final: 14
  residues processed: 312
  average time/residue: 0.2921
  time to fit residues: 116.6124
Evaluate side-chains
  316 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 300
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 THR
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue  141 MET
Chi-restraints excluded: chain B residue  227 PHE
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain C residue  173 LYS
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  199 LEU
Chi-restraints excluded: chain C residue  274 VAL
Chi-restraints excluded: chain D residue   42 SER
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue   78 GLU
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain D residue  233 MET
Chi-restraints excluded: chain D residue  237 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 34 optimal weight:    0.0970
   chunk 103 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 120 optimal weight:    0.5980
   chunk 94 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 23 optimal weight:    0.0980
   chunk 66 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   overall best weight:    0.4178

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.114494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.102769 restraints weight = 13773.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 2.14
r_work: 0.3186 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3031 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.3064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9768  Z= 0.183
  Angle     :  0.524   7.532  13281  Z= 0.263
  Chirality :  0.041   0.160   1541
  Planarity :  0.004   0.038   1696
  Dihedral  :  4.079  18.130   1336
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 19.90 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.25), residues: 1224
  helix:  2.10 (0.20), residues: 668
  sheet: -0.22 (0.56), residues: 94
  loop : -0.45 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 293 
 HIS   0.004   0.001   HIS C  12 
 PHE   0.016   0.001   PHE C  70 
 TYR   0.009   0.001   TYR A 236 
 ARG   0.005   0.000   ARG D 302 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 301
  time to evaluate  : 1.031 
Fit side-chains
REVERT: A   24 PHE cc_start: 0.8420 (t80) cc_final: 0.8215 (t80)
REVERT: A   62 MET cc_start: 0.6755 (mtm) cc_final: 0.6492 (mtm)
REVERT: A   74 MET cc_start: 0.7711 (ppp) cc_final: 0.7135 (ppp)
REVERT: A   95 ARG cc_start: 0.8582 (mtt90) cc_final: 0.8258 (mtt90)
REVERT: A  151 MET cc_start: 0.8573 (mmm) cc_final: 0.8248 (mmp)
REVERT: A  172 MET cc_start: 0.8596 (ppp) cc_final: 0.7933 (ppp)
REVERT: A  185 MET cc_start: 0.7932 (tpp) cc_final: 0.7675 (tpp)
REVERT: A  247 ARG cc_start: 0.8364 (ttp80) cc_final: 0.8054 (ttp80)
REVERT: A  300 ARG cc_start: 0.8471 (ttm-80) cc_final: 0.8075 (mtm-85)
REVERT: B   60 GLN cc_start: 0.8853 (mt0) cc_final: 0.8516 (mt0)
REVERT: B  204 MET cc_start: 0.8024 (ppp) cc_final: 0.7786 (ppp)
REVERT: B  227 PHE cc_start: 0.8285 (m-80) cc_final: 0.7858 (t80)
REVERT: C   16 GLU cc_start: 0.7899 (tp30) cc_final: 0.7556 (tp30)
REVERT: C   24 ASP cc_start: 0.8113 (t0) cc_final: 0.7728 (t0)
REVERT: C   50 SER cc_start: 0.8319 (m) cc_final: 0.7974 (p)
REVERT: C   82 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7463 (mm-30)
REVERT: C  138 VAL cc_start: 0.8460 (m) cc_final: 0.8217 (t)
REVERT: C  149 VAL cc_start: 0.8469 (t) cc_final: 0.8100 (p)
REVERT: C  158 MET cc_start: 0.8319 (mmm) cc_final: 0.7843 (mmm)
REVERT: C  168 ILE cc_start: 0.8703 (tp) cc_final: 0.8387 (pt)
REVERT: C  171 ARG cc_start: 0.8304 (mmt180) cc_final: 0.7881 (mmt90)
REVERT: C  173 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8065 (mtpp)
REVERT: C  198 GLU cc_start: 0.8149 (tp30) cc_final: 0.7804 (tp30)
REVERT: C  201 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8404 (mm-40)
REVERT: C  213 ASP cc_start: 0.7805 (t0) cc_final: 0.7394 (t0)
REVERT: C  234 GLU cc_start: 0.7969 (tt0) cc_final: 0.7408 (tt0)
REVERT: C  314 LYS cc_start: 0.8747 (ttmt) cc_final: 0.8544 (tttt)
REVERT: C  320 ASP cc_start: 0.8475 (p0) cc_final: 0.7987 (p0)
REVERT: D   28 MET cc_start: 0.7106 (tmm) cc_final: 0.6783 (tmm)
REVERT: D   36 LYS cc_start: 0.8433 (mttt) cc_final: 0.8151 (mtmp)
REVERT: D   92 GLN cc_start: 0.7503 (pm20) cc_final: 0.7162 (pm20)
REVERT: D  116 LYS cc_start: 0.8795 (mmmt) cc_final: 0.8521 (mmtm)
REVERT: D  137 ARG cc_start: 0.8448 (mtm-85) cc_final: 0.8200 (mtm180)
REVERT: D  144 MET cc_start: 0.8189 (tpp) cc_final: 0.7743 (mpp)
REVERT: D  177 MET cc_start: 0.8298 (mmm) cc_final: 0.7941 (mmm)
REVERT: D  192 LEU cc_start: 0.8748 (mt) cc_final: 0.8496 (mp)
REVERT: D  210 GLU cc_start: 0.8183 (tt0) cc_final: 0.7957 (tt0)
REVERT: D  252 ASN cc_start: 0.8943 (t0) cc_final: 0.8652 (t0)
  outliers start: 16
  outliers final: 14
  residues processed: 306
  average time/residue: 0.3051
  time to fit residues: 119.7393
Evaluate side-chains
  314 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 299
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  246 THR
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue  141 MET
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain C residue  173 LYS
Chi-restraints excluded: chain C residue  199 LEU
Chi-restraints excluded: chain C residue  274 VAL
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue   78 GLU
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain D residue  233 MET
Chi-restraints excluded: chain D residue  237 LEU
Chi-restraints excluded: chain D residue  329 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 40 optimal weight:    0.5980
   chunk 87 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0010
   chunk 65 optimal weight:    0.6980
   chunk 37 optimal weight:    0.3980
   overall best weight:    0.4786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.113850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.102026 restraints weight = 13931.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 2.15
r_work: 0.3185 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.3154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9768  Z= 0.201
  Angle     :  0.543  10.496  13281  Z= 0.269
  Chirality :  0.041   0.160   1541
  Planarity :  0.004   0.047   1696
  Dihedral  :  4.038  17.958   1336
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 20.49 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.25), residues: 1224
  helix:  2.14 (0.20), residues: 667
  sheet: -0.21 (0.56), residues: 94
  loop : -0.49 (0.29), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 293 
 HIS   0.005   0.001   HIS C  12 
 PHE   0.012   0.001   PHE C  70 
 TYR   0.010   0.001   TYR A 236 
 ARG   0.009   0.000   ARG A 249 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 305
  time to evaluate  : 1.092 
Fit side-chains
REVERT: A   24 PHE cc_start: 0.8415 (t80) cc_final: 0.8211 (t80)
REVERT: A   62 MET cc_start: 0.6680 (mtm) cc_final: 0.6423 (mtm)
REVERT: A   74 MET cc_start: 0.7727 (ppp) cc_final: 0.7163 (ppp)
REVERT: A   95 ARG cc_start: 0.8616 (mtt90) cc_final: 0.8285 (mtt90)
REVERT: A  151 MET cc_start: 0.8592 (mmm) cc_final: 0.8278 (mmp)
REVERT: A  172 MET cc_start: 0.8614 (ppp) cc_final: 0.7965 (ppp)
REVERT: A  185 MET cc_start: 0.7963 (tpp) cc_final: 0.7533 (tpp)
REVERT: A  247 ARG cc_start: 0.8333 (ttp80) cc_final: 0.8018 (ttp80)
REVERT: A  286 SER cc_start: 0.8997 (t) cc_final: 0.8706 (t)
REVERT: A  300 ARG cc_start: 0.8474 (ttm-80) cc_final: 0.8070 (mtm-85)
REVERT: B   60 GLN cc_start: 0.8839 (mt0) cc_final: 0.8515 (mt0)
REVERT: B  204 MET cc_start: 0.8020 (ppp) cc_final: 0.7726 (ppp)
REVERT: B  227 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7804 (t80)
REVERT: C   16 GLU cc_start: 0.7876 (tp30) cc_final: 0.7528 (tp30)
REVERT: C   24 ASP cc_start: 0.8118 (t0) cc_final: 0.7735 (t0)
REVERT: C   50 SER cc_start: 0.8329 (m) cc_final: 0.7984 (p)
REVERT: C   82 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7461 (mm-30)
REVERT: C  138 VAL cc_start: 0.8456 (m) cc_final: 0.8217 (t)
REVERT: C  149 VAL cc_start: 0.8473 (t) cc_final: 0.8097 (p)
REVERT: C  158 MET cc_start: 0.8310 (mmm) cc_final: 0.7835 (mmm)
REVERT: C  168 ILE cc_start: 0.8718 (tp) cc_final: 0.8369 (pt)
REVERT: C  171 ARG cc_start: 0.8303 (mmt180) cc_final: 0.7901 (mmt180)
REVERT: C  173 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8050 (mtpp)
REVERT: C  198 GLU cc_start: 0.8142 (tp30) cc_final: 0.7801 (tp30)
REVERT: C  201 GLN cc_start: 0.8675 (mm-40) cc_final: 0.8410 (mm-40)
REVERT: C  213 ASP cc_start: 0.7821 (t0) cc_final: 0.7413 (t0)
REVERT: C  234 GLU cc_start: 0.7951 (tt0) cc_final: 0.7377 (tt0)
REVERT: C  314 LYS cc_start: 0.8745 (ttmt) cc_final: 0.8511 (tttt)
REVERT: C  320 ASP cc_start: 0.8461 (p0) cc_final: 0.8014 (p0)
REVERT: D   28 MET cc_start: 0.7140 (tmm) cc_final: 0.6837 (tmm)
REVERT: D   36 LYS cc_start: 0.8426 (mttt) cc_final: 0.8148 (mtmp)
REVERT: D   67 LEU cc_start: 0.8246 (mt) cc_final: 0.7847 (mp)
REVERT: D   92 GLN cc_start: 0.7512 (pm20) cc_final: 0.7170 (pm20)
REVERT: D  116 LYS cc_start: 0.8790 (mmmt) cc_final: 0.8512 (mmtm)
REVERT: D  144 MET cc_start: 0.8187 (tpp) cc_final: 0.7736 (mpp)
REVERT: D  177 MET cc_start: 0.8293 (mmm) cc_final: 0.7932 (mmm)
REVERT: D  192 LEU cc_start: 0.8763 (mt) cc_final: 0.8515 (mp)
REVERT: D  210 GLU cc_start: 0.8189 (tt0) cc_final: 0.7968 (tt0)
REVERT: D  226 GLU cc_start: 0.8230 (tt0) cc_final: 0.7946 (tp30)
REVERT: D  252 ASN cc_start: 0.8932 (t0) cc_final: 0.8672 (t0)
REVERT: D  314 LYS cc_start: 0.8606 (ttmm) cc_final: 0.8162 (mtmm)
  outliers start: 22
  outliers final: 13
  residues processed: 314
  average time/residue: 0.2994
  time to fit residues: 119.6849
Evaluate side-chains
  320 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 305
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 THR
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue  141 MET
Chi-restraints excluded: chain B residue  227 PHE
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain C residue  173 LYS
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  199 LEU
Chi-restraints excluded: chain C residue  274 VAL
Chi-restraints excluded: chain D residue   78 GLU
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain D residue  232 VAL
Chi-restraints excluded: chain D residue  233 MET
Chi-restraints excluded: chain D residue  237 LEU
Chi-restraints excluded: chain D residue  329 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 9 optimal weight:    0.2980
   chunk 69 optimal weight:    0.1980
   chunk 55 optimal weight:    0.6980
   chunk 116 optimal weight:    0.2980
   chunk 17 optimal weight:    0.9980
   chunk 98 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 95 optimal weight:    0.5980
   overall best weight:    0.4180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.115739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.104459 restraints weight = 13691.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 1.94
r_work: 0.3217 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.3240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9768  Z= 0.186
  Angle     :  0.535  10.642  13281  Z= 0.265
  Chirality :  0.041   0.158   1541
  Planarity :  0.004   0.043   1696
  Dihedral  :  3.961  18.231   1336
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 21.17 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.25), residues: 1224
  helix:  2.19 (0.20), residues: 667
  sheet: -0.33 (0.52), residues: 104
  loop : -0.46 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 293 
 HIS   0.005   0.001   HIS C  12 
 PHE   0.018   0.001   PHE A  96 
 TYR   0.009   0.001   TYR A 236 
 ARG   0.004   0.000   ARG D 138 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 313
  time to evaluate  : 1.001 
Fit side-chains
REVERT: A   62 MET cc_start: 0.6546 (mtm) cc_final: 0.6304 (mtm)
REVERT: A   74 MET cc_start: 0.7660 (ppp) cc_final: 0.7110 (ppp)
REVERT: A   95 ARG cc_start: 0.8600 (mtt90) cc_final: 0.8290 (mtt90)
REVERT: A  151 MET cc_start: 0.8573 (mmm) cc_final: 0.8251 (mmp)
REVERT: A  172 MET cc_start: 0.8548 (ppp) cc_final: 0.7944 (ppp)
REVERT: A  185 MET cc_start: 0.7878 (tpp) cc_final: 0.7412 (tpp)
REVERT: A  247 ARG cc_start: 0.8265 (ttp80) cc_final: 0.7922 (ttp80)
REVERT: A  286 SER cc_start: 0.8974 (t) cc_final: 0.8661 (t)
REVERT: A  300 ARG cc_start: 0.8448 (ttm-80) cc_final: 0.8041 (mtm-85)
REVERT: B   60 GLN cc_start: 0.8838 (mt0) cc_final: 0.8505 (mt0)
REVERT: B  204 MET cc_start: 0.7959 (ppp) cc_final: 0.7662 (ppp)
REVERT: B  227 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7707 (t80)
REVERT: C   16 GLU cc_start: 0.7869 (tp30) cc_final: 0.7568 (tp30)
REVERT: C   24 ASP cc_start: 0.8067 (t0) cc_final: 0.7604 (t0)
REVERT: C   50 SER cc_start: 0.8213 (m) cc_final: 0.7846 (p)
REVERT: C   82 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7410 (mm-30)
REVERT: C  138 VAL cc_start: 0.8344 (m) cc_final: 0.8143 (t)
REVERT: C  149 VAL cc_start: 0.8379 (t) cc_final: 0.7985 (p)
REVERT: C  158 MET cc_start: 0.8223 (mmm) cc_final: 0.7727 (mmm)
REVERT: C  168 ILE cc_start: 0.8642 (tp) cc_final: 0.8296 (pt)
REVERT: C  171 ARG cc_start: 0.8282 (mmt180) cc_final: 0.7873 (mmt180)
REVERT: C  173 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7955 (mttm)
REVERT: C  198 GLU cc_start: 0.8011 (tp30) cc_final: 0.7668 (tp30)
REVERT: C  201 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8363 (mm-40)
REVERT: C  213 ASP cc_start: 0.7841 (t0) cc_final: 0.7423 (t0)
REVERT: C  234 GLU cc_start: 0.7928 (tt0) cc_final: 0.7284 (tt0)
REVERT: C  314 LYS cc_start: 0.8647 (ttmt) cc_final: 0.8415 (tttt)
REVERT: C  320 ASP cc_start: 0.8379 (p0) cc_final: 0.7947 (p0)
REVERT: D   28 MET cc_start: 0.7050 (tmm) cc_final: 0.6759 (tmm)
REVERT: D   36 LYS cc_start: 0.8395 (mttt) cc_final: 0.8092 (mtmp)
REVERT: D   67 LEU cc_start: 0.8164 (mt) cc_final: 0.7775 (mp)
REVERT: D   92 GLN cc_start: 0.7501 (pm20) cc_final: 0.7173 (pm20)
REVERT: D  116 LYS cc_start: 0.8748 (mmmt) cc_final: 0.8477 (mmtm)
REVERT: D  129 ASN cc_start: 0.8451 (m-40) cc_final: 0.8148 (m110)
REVERT: D  144 MET cc_start: 0.8089 (tpp) cc_final: 0.7617 (mpp)
REVERT: D  177 MET cc_start: 0.8263 (mmm) cc_final: 0.7937 (mmm)
REVERT: D  192 LEU cc_start: 0.8696 (mt) cc_final: 0.8427 (mp)
REVERT: D  210 GLU cc_start: 0.8125 (tt0) cc_final: 0.7890 (tt0)
REVERT: D  226 GLU cc_start: 0.8095 (tt0) cc_final: 0.7812 (tt0)
REVERT: D  252 ASN cc_start: 0.8897 (t0) cc_final: 0.8622 (t0)
REVERT: D  314 LYS cc_start: 0.8546 (ttmm) cc_final: 0.8049 (mtmm)
  outliers start: 19
  outliers final: 15
  residues processed: 321
  average time/residue: 0.2955
  time to fit residues: 121.7137
Evaluate side-chains
  330 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 313
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  246 THR
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  227 PHE
Chi-restraints excluded: chain C residue  173 LYS
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  199 LEU
Chi-restraints excluded: chain C residue  274 VAL
Chi-restraints excluded: chain D residue   78 GLU
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain D residue  232 VAL
Chi-restraints excluded: chain D residue  233 MET
Chi-restraints excluded: chain D residue  237 LEU
Chi-restraints excluded: chain D residue  267 ARG
Chi-restraints excluded: chain D residue  329 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 99 optimal weight:    0.6980
   chunk 95 optimal weight:    0.6980
   chunk 105 optimal weight:    1.9990
   chunk 82 optimal weight:    0.7980
   chunk 81 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 85 optimal weight:    0.4980
   chunk 45 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9990
   chunk 69 optimal weight:    0.1980
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.114977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.103764 restraints weight = 13769.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 1.94
r_work: 0.3199 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3050 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.3258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9768  Z= 0.228
  Angle     :  0.560  11.246  13281  Z= 0.277
  Chirality :  0.042   0.158   1541
  Planarity :  0.004   0.041   1696
  Dihedral  :  3.974  18.474   1336
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 21.46 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.25), residues: 1224
  helix:  2.14 (0.20), residues: 673
  sheet: -0.38 (0.52), residues: 104
  loop : -0.50 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 293 
 HIS   0.006   0.001   HIS C  12 
 PHE   0.025   0.001   PHE A 109 
 TYR   0.010   0.001   TYR A 236 
 ARG   0.011   0.000   ARG A 249 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  334 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 315
  time to evaluate  : 1.121 
Fit side-chains
REVERT: A   62 MET cc_start: 0.6571 (mtm) cc_final: 0.6335 (mtm)
REVERT: A   74 MET cc_start: 0.7671 (ppp) cc_final: 0.7409 (ppp)
REVERT: A   95 ARG cc_start: 0.8605 (mtt90) cc_final: 0.8296 (mtt90)
REVERT: A  151 MET cc_start: 0.8504 (mmm) cc_final: 0.8172 (mmp)
REVERT: A  172 MET cc_start: 0.8590 (ppp) cc_final: 0.7958 (ppp)
REVERT: A  185 MET cc_start: 0.7933 (tpp) cc_final: 0.7441 (tpp)
REVERT: A  247 ARG cc_start: 0.8264 (ttp80) cc_final: 0.7926 (ttp80)
REVERT: A  286 SER cc_start: 0.9001 (t) cc_final: 0.8712 (t)
REVERT: B   60 GLN cc_start: 0.8827 (mt0) cc_final: 0.8506 (mt0)
REVERT: B  204 MET cc_start: 0.7976 (ppp) cc_final: 0.7690 (ppp)
REVERT: B  227 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7752 (t80)
REVERT: C   16 GLU cc_start: 0.7885 (tp30) cc_final: 0.7472 (tp30)
REVERT: C   24 ASP cc_start: 0.8036 (t0) cc_final: 0.7609 (t0)
REVERT: C   50 SER cc_start: 0.8277 (m) cc_final: 0.7923 (p)
REVERT: C   82 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7447 (mm-30)
REVERT: C  138 VAL cc_start: 0.8393 (m) cc_final: 0.8167 (t)
REVERT: C  149 VAL cc_start: 0.8444 (t) cc_final: 0.8075 (p)
REVERT: C  158 MET cc_start: 0.8267 (mmm) cc_final: 0.7769 (mmm)
REVERT: C  168 ILE cc_start: 0.8677 (tp) cc_final: 0.8322 (pt)
REVERT: C  171 ARG cc_start: 0.8302 (mmt180) cc_final: 0.7891 (mmt180)
REVERT: C  173 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8004 (mttm)
REVERT: C  198 GLU cc_start: 0.8022 (tp30) cc_final: 0.7680 (tp30)
REVERT: C  201 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8377 (mm-40)
REVERT: C  213 ASP cc_start: 0.7856 (t0) cc_final: 0.7454 (t0)
REVERT: C  234 GLU cc_start: 0.7863 (tt0) cc_final: 0.7238 (tt0)
REVERT: C  320 ASP cc_start: 0.8368 (p0) cc_final: 0.7946 (p0)
REVERT: D   28 MET cc_start: 0.7065 (tmm) cc_final: 0.6783 (tmm)
REVERT: D   36 LYS cc_start: 0.8405 (mttt) cc_final: 0.8113 (mtmp)
REVERT: D   92 GLN cc_start: 0.7478 (pm20) cc_final: 0.7169 (pm20)
REVERT: D  116 LYS cc_start: 0.8740 (mmmt) cc_final: 0.8489 (mmtm)
REVERT: D  129 ASN cc_start: 0.8482 (m-40) cc_final: 0.8168 (m110)
REVERT: D  144 MET cc_start: 0.8094 (tpp) cc_final: 0.7632 (mpp)
REVERT: D  177 MET cc_start: 0.8306 (mmm) cc_final: 0.7955 (mmm)
REVERT: D  192 LEU cc_start: 0.8741 (mt) cc_final: 0.8489 (mp)
REVERT: D  210 GLU cc_start: 0.8147 (tt0) cc_final: 0.7917 (tt0)
REVERT: D  226 GLU cc_start: 0.8124 (tt0) cc_final: 0.7830 (tt0)
REVERT: D  252 ASN cc_start: 0.8917 (t0) cc_final: 0.8523 (t0)
REVERT: D  314 LYS cc_start: 0.8554 (ttmm) cc_final: 0.8087 (mtmm)
  outliers start: 19
  outliers final: 16
  residues processed: 323
  average time/residue: 0.2926
  time to fit residues: 120.9313
Evaluate side-chains
  329 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 311
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  246 THR
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  227 PHE
Chi-restraints excluded: chain C residue  173 LYS
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  199 LEU
Chi-restraints excluded: chain C residue  274 VAL
Chi-restraints excluded: chain D residue   42 SER
Chi-restraints excluded: chain D residue   78 GLU
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain D residue  232 VAL
Chi-restraints excluded: chain D residue  233 MET
Chi-restraints excluded: chain D residue  237 LEU
Chi-restraints excluded: chain D residue  267 ARG
Chi-restraints excluded: chain D residue  329 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 111 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9980
   chunk 34 optimal weight:    0.3980
   chunk 20 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 83 optimal weight:    0.8980
   chunk 84 optimal weight:    0.8980
   chunk 6 optimal weight:    0.4980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
D  14 GLN
D  44 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.114823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.103474 restraints weight = 13741.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 1.96
r_work: 0.3199 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3051 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.3302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9768  Z= 0.238
  Angle     :  0.563  10.963  13281  Z= 0.279
  Chirality :  0.042   0.160   1541
  Planarity :  0.004   0.041   1696
  Dihedral  :  3.990  18.125   1336
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 21.27 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.25), residues: 1224
  helix:  2.15 (0.20), residues: 673
  sheet: -0.37 (0.52), residues: 104
  loop : -0.48 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 293 
 HIS   0.006   0.001   HIS C  12 
 PHE   0.024   0.002   PHE A  96 
 TYR   0.010   0.001   TYR A 236 
 ARG   0.004   0.000   ARG C 266 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5504.29 seconds
wall clock time: 97 minutes 48.31 seconds (5868.31 seconds total)