Starting phenix.real_space_refine
on Wed Feb 12 11:46:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6kmf_0724/02_2025/6kmf_0724.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6kmf_0724/02_2025/6kmf_0724.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6kmf_0724/02_2025/6kmf_0724.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6kmf_0724/02_2025/6kmf_0724.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6kmf_0724/02_2025/6kmf_0724.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6kmf_0724/02_2025/6kmf_0724.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    4860      2.51       5
     N    1293      2.21       5
     O    1524      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7704
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2403
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2403
          Classifications: {'peptide': 316}
          Link IDs: {'PTRANS': 13, 'TRANS': 302}
    Chain: "B"
      Number of atoms: 2568
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2568
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 323}
    Chain: "C"
      Number of atoms: 2568
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2568
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 323}
    Chain: "D"
      Number of atoms: 165
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 165
          Classifications: {'peptide': 21}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 20}
  Time building chain proxies: 6.29, per 1000 atoms: 0.82
  Number of scatterers: 7704
  At special positions: 0
  Unit cell: (170.24, 73.92, 181.44, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      27     16.00
     O    1524      8.00
     N    1293      7.00
     C    4860      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.78
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1866

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 20 sheets defined
      7.2% alpha, 26.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 109 through 114
    Processing helix  chain 'A' and resid 121 through 127
      removed outlier: 3.694A  pdb=" N   GLN A 125 " --> pdb=" O   ALA A 122 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   GLU A 126 " --> pdb=" O   GLU A 123 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ALA A 127 " --> pdb=" O   ASN A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 187
      removed outlier: 3.525A  pdb=" N   TYR A 186 " --> pdb=" O   SER A 183 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ASP A 187 " --> pdb=" O   ALA A 184 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 183 through 187'
    Processing helix  chain 'A' and resid 291 through 293
      No H-bonds generated for 'chain 'A' and resid 291 through 293'
    Processing helix  chain 'A' and resid 294 through 299
    Processing helix  chain 'B' and resid 109 through 115
    Processing helix  chain 'B' and resid 121 through 125
      removed outlier: 3.716A  pdb=" N   ASN B 124 " --> pdb=" O   THR B 121 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLN B 125 " --> pdb=" O   ALA B 122 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 121 through 125'
    Processing helix  chain 'B' and resid 294 through 301
      removed outlier: 3.839A  pdb=" N   ALA B 300 " --> pdb=" O   ALA B 296 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ALA B 301 " --> pdb=" O   ALA B 297 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 109 through 114
      removed outlier: 3.570A  pdb=" N   LYS C 114 " --> pdb=" O   LEU C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 121 through 126
      removed outlier: 3.700A  pdb=" N   GLN C 125 " --> pdb=" O   ALA C 122 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   GLU C 126 " --> pdb=" O   GLU C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 183 through 187
      removed outlier: 3.680A  pdb=" N   TYR C 186 " --> pdb=" O   SER C 183 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ASP C 187 " --> pdb=" O   ALA C 184 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 183 through 187'
    Processing helix  chain 'C' and resid 294 through 299
      removed outlier: 3.983A  pdb=" N   GLN C 299 " --> pdb=" O   LEU C 295 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 300 through 302
      No H-bonds generated for 'chain 'C' and resid 300 through 302'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 74
      removed outlier: 5.895A  pdb=" N   LEU A 164 " --> pdb=" O   THR B 370 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ALA B 363 " --> pdb=" O   CYS A  87 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   CYS A  87 " --> pdb=" O   ALA B 363 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   VAL B 367 " --> pdb=" O   GLU A  83 " (cutoff:3.500A)
      removed outlier: 5.451A  pdb=" N   GLU A  83 " --> pdb=" O   VAL B 367 " (cutoff:3.500A)
      removed outlier: 8.660A  pdb=" N   CYS B 369 " --> pdb=" O   LYS A  81 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   LYS A  81 " --> pdb=" O   CYS B 369 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 74
      removed outlier: 5.895A  pdb=" N   LEU A 164 " --> pdb=" O   THR B 370 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ASN B 366 " --> pdb=" O   ASN A 146 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   TYR A 147 " --> pdb=" O   ASN A 157 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.767A  pdb=" N   THR A 118 " --> pdb=" O   SER A 206 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   SER A 206 " --> pdb=" O   THR A 118 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 256 through 260
      removed outlier: 3.669A  pdb=" N   GLN A 256 " --> pdb=" O   PHE A 175 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   ARG A 172 " --> pdb=" O   TYR A 341 " (cutoff:3.500A)
      removed outlier: 7.810A  pdb=" N   ILE A 343 " --> pdb=" O   ARG A 172 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   ALA A 174 " --> pdb=" O   ILE A 343 " (cutoff:3.500A)
      removed outlier: 8.157A  pdb=" N   LEU A 345 " --> pdb=" O   ALA A 174 " (cutoff:3.500A)
      removed outlier: 8.016A  pdb=" N   THR A 176 " --> pdb=" O   LEU A 345 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   GLN B 379 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   ASP A 342 " --> pdb=" O   GLN B 379 " (cutoff:3.500A)
      removed outlier: 7.158A  pdb=" N   ALA B 381 " --> pdb=" O   ASP A 342 " (cutoff:3.500A)
      removed outlier: 6.136A  pdb=" N   LYS A 344 " --> pdb=" O   ALA B 381 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 190 through 196
      removed outlier: 3.627A  pdb=" N   VAL A 193 " --> pdb=" O   LYS A 282 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   TYR A 280 " --> pdb=" O   GLU A 195 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL A 279 " --> pdb=" O   TYR A 312 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 70 through 77
      removed outlier: 3.575A  pdb=" N   LYS B  74 " --> pdb=" O   VAL B  62 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   VAL B  62 " --> pdb=" O   LYS B  74 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ALA B  98 " --> pdb=" O   MET B 132 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 81 through 82
      removed outlier: 3.699A  pdb=" N   VAL C 367 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
      removed outlier: 5.927A  pdb=" N   LEU B 164 " --> pdb=" O   THR C 370 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 91
      removed outlier: 3.649A  pdb=" N   GLY B  90 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 118 through 119
    Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147
      removed outlier: 3.598A  pdb=" N   TYR B 147 " --> pdb=" O   ASN B 157 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 257 through 260
      removed outlier: 6.567A  pdb=" N   ARG B 172 " --> pdb=" O   TYR B 341 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   ILE B 343 " --> pdb=" O   ARG B 172 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   ALA B 174 " --> pdb=" O   ILE B 343 " (cutoff:3.500A)
      removed outlier: 7.953A  pdb=" N   LEU B 345 " --> pdb=" O   ALA B 174 " (cutoff:3.500A)
      removed outlier: 7.761A  pdb=" N   THR B 176 " --> pdb=" O   LEU B 345 " (cutoff:3.500A)
      removed outlier: 11.913A  pdb=" N   ILE B 347 " --> pdb=" O   THR B 176 " (cutoff:3.500A)
      removed outlier: 5.975A  pdb=" N   LYS B 340 " --> pdb=" O   VAL C 377 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   GLN C 379 " --> pdb=" O   LYS B 340 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   ASP B 342 " --> pdb=" O   GLN C 379 " (cutoff:3.500A)
      removed outlier: 7.980A  pdb=" N   ALA C 381 " --> pdb=" O   ASP B 342 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   LYS B 344 " --> pdb=" O   ALA C 381 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   TRP C 383 " --> pdb=" O   LYS B 344 " (cutoff:3.500A)
      removed outlier: 5.711A  pdb=" N   THR B 346 " --> pdb=" O   TRP C 383 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 190 through 192
    Processing sheet with id=AB4, first strand: chain 'B' and resid 263 through 264
      removed outlier: 3.669A  pdb=" N   ASN B 263 " --> pdb=" O   ILE B 335 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 70 through 73
      removed outlier: 4.398A  pdb=" N   ALA C  72 " --> pdb=" O   VAL C  64 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   VAL C  64 " --> pdb=" O   ALA C  72 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   LEU C 164 " --> pdb=" O   THR D 370 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ILE C  85 " --> pdb=" O   LEU D 365 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   VAL D 367 " --> pdb=" O   GLU C  83 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   GLU C  83 " --> pdb=" O   VAL D 367 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   CYS D 369 " --> pdb=" O   LYS C  81 " (cutoff:3.500A)
      removed outlier: 6.084A  pdb=" N   LYS C  81 " --> pdb=" O   CYS D 369 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 90 through 91
    Processing sheet with id=AB7, first strand: chain 'C' and resid 146 through 147
    Processing sheet with id=AB8, first strand: chain 'C' and resid 256 through 260
      removed outlier: 3.955A  pdb=" N   GLN C 256 " --> pdb=" O   PHE C 175 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   ARG C 172 " --> pdb=" O   TYR C 341 " (cutoff:3.500A)
      removed outlier: 7.850A  pdb=" N   ILE C 343 " --> pdb=" O   ARG C 172 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   ALA C 174 " --> pdb=" O   ILE C 343 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   LEU C 345 " --> pdb=" O   ALA C 174 " (cutoff:3.500A)
      removed outlier: 7.745A  pdb=" N   THR C 176 " --> pdb=" O   LEU C 345 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 190 through 196
      removed outlier: 5.585A  pdb=" N   PHE C 192 " --> pdb=" O   GLN C 284 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   GLN C 284 " --> pdb=" O   PHE C 192 " (cutoff:3.500A)
      removed outlier: 6.067A  pdb=" N   LYS C 282 " --> pdb=" O   PRO C 194 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 221 through 222
      removed outlier: 3.564A  pdb=" N   THR C 222 " --> pdb=" O   ALA C 238 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC1
    Processing sheet with id=AC2, first strand: chain 'C' and resid 263 through 264
      removed outlier: 3.502A  pdb=" N   ASN C 263 " --> pdb=" O   ILE C 335 " (cutoff:3.500A)

    125 hydrogen bonds defined for protein.
    327 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.98

  Time building geometry restraints manager: 2.11 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2296
        1.33 -     1.45: 1137
        1.45 -     1.57: 4378
        1.57 -     1.68: 0
        1.68 -     1.80: 45
  Bond restraints: 7856
  Sorted by residual:
  bond pdb=" N   THR B 138 "
       pdb=" CA  THR B 138 "
    ideal  model  delta    sigma   weight residual
    1.460  1.487 -0.027 1.42e-02 4.96e+03 3.64e+00
  bond pdb=" N   THR C 138 "
       pdb=" CA  THR C 138 "
    ideal  model  delta    sigma   weight residual
    1.457  1.478 -0.020 1.29e-02 6.01e+03 2.47e+00
  bond pdb=" N   THR A 138 "
       pdb=" CA  THR A 138 "
    ideal  model  delta    sigma   weight residual
    1.457  1.477 -0.020 1.29e-02 6.01e+03 2.37e+00
  bond pdb=" CG  LEU C 315 "
       pdb=" CD1 LEU C 315 "
    ideal  model  delta    sigma   weight residual
    1.521  1.474  0.047 3.30e-02 9.18e+02 2.06e+00
  bond pdb=" N   ASN B 286 "
       pdb=" CA  ASN B 286 "
    ideal  model  delta    sigma   weight residual
    1.460  1.479 -0.020 1.42e-02 4.96e+03 1.89e+00
  ... (remaining 7851 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.04: 10309
        2.04 -     4.07: 323
        4.07 -     6.11: 50
        6.11 -     8.15: 16
        8.15 -    10.18: 6
  Bond angle restraints: 10704
  Sorted by residual:
  angle pdb=" C   LEU C 225 "
        pdb=" N   THR C 226 "
        pdb=" CA  THR C 226 "
      ideal   model   delta    sigma   weight residual
     122.08  128.86   -6.78 1.47e+00 4.63e-01 2.13e+01
  angle pdb=" C   LYS A 137 "
        pdb=" N   THR A 138 "
        pdb=" CA  THR A 138 "
      ideal   model   delta    sigma   weight residual
     121.54  129.72   -8.18 1.91e+00 2.74e-01 1.84e+01
  angle pdb=" C   GLY A 149 "
        pdb=" N   TYR A 150 "
        pdb=" CA  TYR A 150 "
      ideal   model   delta    sigma   weight residual
     122.46  128.36   -5.90 1.41e+00 5.03e-01 1.75e+01
  angle pdb=" C   LYS C 137 "
        pdb=" N   THR C 138 "
        pdb=" CA  THR C 138 "
      ideal   model   delta    sigma   weight residual
     121.54  129.42   -7.88 1.91e+00 2.74e-01 1.70e+01
  angle pdb=" C   LYS B 137 "
        pdb=" N   THR B 138 "
        pdb=" CA  THR B 138 "
      ideal   model   delta    sigma   weight residual
     122.82  128.56   -5.74 1.42e+00 4.96e-01 1.63e+01
  ... (remaining 10699 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.62: 4121
       16.62 -    33.24: 442
       33.24 -    49.86: 76
       49.86 -    66.49: 21
       66.49 -    83.11: 10
  Dihedral angle restraints: 4670
    sinusoidal: 1740
      harmonic: 2930
  Sorted by residual:
  dihedral pdb=" CA  VAL A 248 "
           pdb=" C   VAL A 248 "
           pdb=" N   ALA A 249 "
           pdb=" CA  ALA A 249 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.91   24.09     0      5.00e+00 4.00e-02 2.32e+01
  dihedral pdb=" CA  GLY A 199 "
           pdb=" C   GLY A 199 "
           pdb=" N   LEU A 200 "
           pdb=" CA  LEU A 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.25  -23.75     0      5.00e+00 4.00e-02 2.26e+01
  dihedral pdb=" CA  ASN A 246 "
           pdb=" C   ASN A 246 "
           pdb=" N   TYR A 247 "
           pdb=" CA  TYR A 247 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.94  -23.06     0      5.00e+00 4.00e-02 2.13e+01
  ... (remaining 4667 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 907
       0.058 -    0.116: 242
       0.116 -    0.174: 50
       0.174 -    0.232: 15
       0.232 -    0.290: 4
  Chirality restraints: 1218
  Sorted by residual:
  chirality pdb=" CB  ILE B 197 "
            pdb=" CA  ILE B 197 "
            pdb=" CG1 ILE B 197 "
            pdb=" CG2 ILE B 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.29 2.00e-01 2.50e+01 2.10e+00
  chirality pdb=" CB  ILE C 148 "
            pdb=" CA  ILE C 148 "
            pdb=" CG1 ILE C 148 "
            pdb=" CG2 ILE C 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" CB  ILE A 178 "
            pdb=" CA  ILE A 178 "
            pdb=" CG1 ILE A 178 "
            pdb=" CG2 ILE A 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.89   -0.25 2.00e-01 2.50e+01 1.50e+00
  ... (remaining 1215 not shown)

  Planarity restraints: 1397
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 193 "    0.044 5.00e-02 4.00e+02   6.66e-02 7.11e+00
        pdb=" N   PRO A 194 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO A 194 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 194 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 248 "    0.013 2.00e-02 2.50e+03   2.65e-02 7.01e+00
        pdb=" C   VAL A 248 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   VAL A 248 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ALA A 249 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 233 "   -0.032 5.00e-02 4.00e+02   4.88e-02 3.80e+00
        pdb=" N   PRO B 234 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B 234 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 234 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 1394 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2397
        2.82 -     3.34: 6458
        3.34 -     3.86: 11953
        3.86 -     4.38: 12372
        4.38 -     4.90: 22342
  Nonbonded interactions: 55522
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 147 "
            pdb=" O   GLU C 155 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" O   SER B 266 "
            pdb=" OG  SER B 266 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" ND2 ASN A 146 "
            pdb=" OD1 ASN A 157 "
     model   vdw
     2.315 3.120
  nonbonded pdb=" O   LEU C 200 "
            pdb=" OG1 THR C 222 "
     model   vdw
     2.372 3.040
  nonbonded pdb=" O   THR B  80 "
            pdb=" OG1 THR B  80 "
     model   vdw
     2.373 3.040
  ... (remaining 55517 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and resid 47 through 362)
  selection = (chain 'C' and resid 47 through 362)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.150
  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:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     22.080
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.030
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
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      :  0.006   0.047   7856  Z= 0.380
  Angle     :  0.901  10.181  10704  Z= 0.492
  Chirality :  0.058   0.290   1218
  Planarity :  0.006   0.067   1397
  Dihedral  : 14.663  83.107   2804
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.36 %
    Favored  : 86.64 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 14.80 %
    Favored  : 84.58 %
  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: -4.41 (0.21), residues: 1003
  helix: -4.98 (0.23), residues: 54
  sheet: -1.79 (0.44), residues: 144
  loop : -3.32 (0.17), residues: 805

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 242 
 HIS   0.003   0.001   HIS B 364 
 PHE   0.011   0.002   PHE B 318 
 TYR   0.030   0.003   TYR C 150 
 ARG   0.003   0.001   ARG A 172 

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 221
  time to evaluate  : 0.846 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8511 (tttm) cc_final: 0.8212 (tppt)
REVERT: A   97 MET cc_start: 0.8361 (mtp) cc_final: 0.8097 (mtt)
REVERT: A  119 GLU cc_start: 0.8774 (mp0) cc_final: 0.8521 (mt-10)
REVERT: A  124 ASN cc_start: 0.9007 (m110) cc_final: 0.8525 (m110)
REVERT: A  182 MET cc_start: 0.8145 (mmt) cc_final: 0.7850 (mmt)
REVERT: A  200 LEU cc_start: 0.8614 (mt) cc_final: 0.8380 (mt)
REVERT: A  258 PHE cc_start: 0.8922 (m-80) cc_final: 0.8216 (m-80)
REVERT: A  259 TYR cc_start: 0.8845 (m-80) cc_final: 0.8619 (m-80)
REVERT: A  318 PHE cc_start: 0.8582 (t80) cc_final: 0.8088 (t80)
REVERT: B   92 ARG cc_start: 0.8386 (mmt-90) cc_final: 0.8122 (mmt-90)
REVERT: B  131 ILE cc_start: 0.8694 (mt) cc_final: 0.8492 (mp)
REVERT: B  195 GLU cc_start: 0.8091 (tp30) cc_final: 0.7828 (tp30)
REVERT: B  256 GLN cc_start: 0.8968 (mm110) cc_final: 0.8710 (mm-40)
REVERT: B  317 ASN cc_start: 0.8224 (t0) cc_final: 0.7981 (t0)
REVERT: B  329 TYR cc_start: 0.9064 (t80) cc_final: 0.8804 (t80)
REVERT: B  354 ASN cc_start: 0.8154 (t0) cc_final: 0.7870 (t0)
REVERT: C   53 ASP cc_start: 0.8274 (m-30) cc_final: 0.7866 (t0)
REVERT: C   83 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6971 (mm-30)
REVERT: C  236 ASN cc_start: 0.8181 (t0) cc_final: 0.7587 (t0)
  outliers start: 5
  outliers final: 2
  residues processed: 225
  average time/residue: 0.1755
  time to fit residues: 54.3884
Evaluate side-chains
  183 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 181
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain B residue  316 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    0.6980
   chunk 75 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0470
   chunk 50 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 77 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   chunk 89 optimal weight:    4.9990
   overall best weight:    1.1484

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN
A 286 ASN
A 333 ASN
** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 146 ASN
B 161 ASN
** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 219 ASN
B 286 ASN
C 219 ASN
C 236 ASN
C 286 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.124950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.107215 restraints weight = 13603.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.110899 restraints weight = 6946.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.113430 restraints weight = 4304.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.1472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7856  Z= 0.179
  Angle     :  0.601   9.382  10704  Z= 0.320
  Chirality :  0.044   0.259   1218
  Planarity :  0.004   0.076   1397
  Dihedral  :  5.885  53.832   1084
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.47 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 18.41 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.85 (0.23), residues: 1003
  helix: -4.22 (0.41), residues: 55
  sheet: -1.31 (0.44), residues: 148
  loop : -2.96 (0.19), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 242 
 HIS   0.002   0.001   HIS A 158 
 PHE   0.010   0.001   PHE C  48 
 TYR   0.019   0.001   TYR B 198 
 ARG   0.003   0.001   ARG C 337 

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 205
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.6997 (p0)
REVERT: A   56 LYS cc_start: 0.8468 (tttm) cc_final: 0.8178 (tppt)
REVERT: A   80 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8128 (m)
REVERT: A   97 MET cc_start: 0.8234 (mtp) cc_final: 0.7929 (mtt)
REVERT: A  124 ASN cc_start: 0.9010 (m110) cc_final: 0.8602 (m110)
REVERT: A  182 MET cc_start: 0.8297 (mmt) cc_final: 0.7971 (mmt)
REVERT: A  213 LEU cc_start: 0.9111 (pt) cc_final: 0.8638 (pp)
REVERT: A  258 PHE cc_start: 0.8755 (m-80) cc_final: 0.8010 (m-80)
REVERT: A  318 PHE cc_start: 0.8493 (t80) cc_final: 0.7942 (t80)
REVERT: B  195 GLU cc_start: 0.8211 (tp30) cc_final: 0.7938 (tp30)
REVERT: B  256 GLN cc_start: 0.9002 (mm110) cc_final: 0.8701 (mm-40)
REVERT: B  317 ASN cc_start: 0.8176 (t0) cc_final: 0.7952 (t0)
REVERT: B  329 TYR cc_start: 0.9008 (t80) cc_final: 0.8594 (t80)
REVERT: B  348 THR cc_start: 0.8626 (m) cc_final: 0.8401 (p)
REVERT: B  354 ASN cc_start: 0.8164 (t0) cc_final: 0.7947 (t0)
REVERT: C   53 ASP cc_start: 0.8226 (m-30) cc_final: 0.7828 (t0)
REVERT: C   83 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6817 (mm-30)
REVERT: D  368 GLN cc_start: 0.7260 (tm-30) cc_final: 0.6799 (tm-30)
  outliers start: 30
  outliers final: 18
  residues processed: 221
  average time/residue: 0.1448
  time to fit residues: 46.9213
Evaluate side-chains
  202 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 182
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain C residue  278 CYS
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  330 THR
Chi-restraints excluded: chain C residue  335 ILE
Chi-restraints excluded: chain C residue  359 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 11 optimal weight:   20.0000
   chunk 53 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 76 optimal weight:    3.9990
   chunk 24 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 205 GLN
A 333 ASN
B 157 ASN
B 219 ASN
C 146 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.124070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.106177 restraints weight = 14127.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.109984 restraints weight = 6936.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.112599 restraints weight = 4217.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.1706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7856  Z= 0.205
  Angle     :  0.602   9.537  10704  Z= 0.319
  Chirality :  0.044   0.267   1218
  Planarity :  0.004   0.076   1397
  Dihedral  :  5.620  48.211   1084
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.97 %
    Favored  : 90.03 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 18.78 %
    Favored  : 76.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.64 (0.24), residues: 1003
  helix: -3.66 (0.45), residues: 61
  sheet: -1.38 (0.45), residues: 144
  loop : -2.77 (0.19), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 242 
 HIS   0.002   0.001   HIS A 158 
 PHE   0.019   0.002   PHE C 192 
 TYR   0.022   0.002   TYR B 198 
 ARG   0.006   0.000   ARG B  92 

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 193
  time to evaluate  : 0.828 
Fit side-chains
REVERT: A   53 ASP cc_start: 0.7478 (m-30) cc_final: 0.7085 (p0)
REVERT: A   56 LYS cc_start: 0.8466 (tttm) cc_final: 0.8169 (tppt)
REVERT: A   80 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8132 (m)
REVERT: A   97 MET cc_start: 0.8191 (mtp) cc_final: 0.7895 (mtt)
REVERT: A  124 ASN cc_start: 0.9105 (m110) cc_final: 0.8650 (m110)
REVERT: A  182 MET cc_start: 0.8355 (mmt) cc_final: 0.8057 (mmt)
REVERT: A  213 LEU cc_start: 0.9231 (pt) cc_final: 0.8658 (pp)
REVERT: A  258 PHE cc_start: 0.8705 (m-80) cc_final: 0.7978 (m-80)
REVERT: A  318 PHE cc_start: 0.8580 (t80) cc_final: 0.7980 (t80)
REVERT: A  329 TYR cc_start: 0.8373 (t80) cc_final: 0.7941 (t80)
REVERT: B  195 GLU cc_start: 0.8123 (tp30) cc_final: 0.7837 (tp30)
REVERT: B  256 GLN cc_start: 0.9002 (mm110) cc_final: 0.8684 (mm-40)
REVERT: B  317 ASN cc_start: 0.8238 (t0) cc_final: 0.7901 (t0)
REVERT: B  329 TYR cc_start: 0.9014 (t80) cc_final: 0.8566 (t80)
REVERT: B  348 THR cc_start: 0.8592 (m) cc_final: 0.8352 (p)
REVERT: B  354 ASN cc_start: 0.8209 (t0) cc_final: 0.7987 (t0)
REVERT: C   53 ASP cc_start: 0.8355 (m-30) cc_final: 0.7818 (t0)
REVERT: C   83 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6821 (mm-30)
REVERT: C  146 ASN cc_start: 0.7057 (OUTLIER) cc_final: 0.6844 (p0)
REVERT: D  368 GLN cc_start: 0.7352 (tm-30) cc_final: 0.6839 (tm-30)
  outliers start: 41
  outliers final: 29
  residues processed: 212
  average time/residue: 0.1446
  time to fit residues: 44.9484
Evaluate side-chains
  203 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 172
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  361 GLU
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  146 ASN
Chi-restraints excluded: chain C residue  148 ILE
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain C residue  278 CYS
Chi-restraints excluded: chain C residue  314 VAL
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  330 THR
Chi-restraints excluded: chain C residue  335 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 19 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 32 optimal weight:    3.9990
   chunk 71 optimal weight:    9.9990
   chunk 5 optimal weight:    0.8980
   chunk 31 optimal weight:    4.9990
   chunk 48 optimal weight:    9.9990
   chunk 63 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 205 GLN
A 333 ASN
A 357 ASN
** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 219 ASN
C  78 ASN
C 146 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.122760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.105039 restraints weight = 13836.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.108792 restraints weight = 6856.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.111342 restraints weight = 4170.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.1813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7856  Z= 0.230
  Angle     :  0.605  10.133  10704  Z= 0.320
  Chirality :  0.045   0.266   1218
  Planarity :  0.004   0.076   1397
  Dihedral  :  5.623  45.094   1084
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.97 %
    Favored  : 90.03 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 18.78 %
    Favored  : 76.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.50 (0.24), residues: 1003
  helix: -3.27 (0.50), residues: 61
  sheet: -1.40 (0.45), residues: 144
  loop : -2.68 (0.20), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 242 
 HIS   0.003   0.001   HIS A 158 
 PHE   0.021   0.002   PHE C 192 
 TYR   0.022   0.002   TYR B 198 
 ARG   0.003   0.000   ARG C 245 

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 179
  time to evaluate  : 0.812 
Fit side-chains
REVERT: A   53 ASP cc_start: 0.7412 (m-30) cc_final: 0.7103 (p0)
REVERT: A   56 LYS cc_start: 0.8477 (tttm) cc_final: 0.8223 (tppt)
REVERT: A   80 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8183 (m)
REVERT: A   97 MET cc_start: 0.8178 (mtp) cc_final: 0.7868 (mtt)
REVERT: A  124 ASN cc_start: 0.9013 (m110) cc_final: 0.8581 (m110)
REVERT: A  182 MET cc_start: 0.8356 (mmt) cc_final: 0.8073 (mmt)
REVERT: A  213 LEU cc_start: 0.9257 (pt) cc_final: 0.8612 (pp)
REVERT: A  318 PHE cc_start: 0.8628 (t80) cc_final: 0.8052 (t80)
REVERT: A  329 TYR cc_start: 0.8420 (t80) cc_final: 0.8027 (t80)
REVERT: B  195 GLU cc_start: 0.8137 (tp30) cc_final: 0.7848 (tp30)
REVERT: B  256 GLN cc_start: 0.9008 (mm110) cc_final: 0.8720 (mm-40)
REVERT: B  262 GLU cc_start: 0.8113 (tp30) cc_final: 0.7850 (mm-30)
REVERT: B  329 TYR cc_start: 0.9013 (t80) cc_final: 0.8555 (t80)
REVERT: B  348 THR cc_start: 0.8596 (m) cc_final: 0.8352 (p)
REVERT: B  354 ASN cc_start: 0.8236 (t0) cc_final: 0.8002 (t0)
REVERT: C   83 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6806 (mm-30)
REVERT: C   91 GLN cc_start: 0.7224 (tp-100) cc_final: 0.6834 (tp-100)
  outliers start: 42
  outliers final: 34
  residues processed: 196
  average time/residue: 0.1440
  time to fit residues: 41.3762
Evaluate side-chains
  207 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 172
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  205 GLN
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  361 GLU
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  360 THR
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  148 ILE
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain C residue  276 ILE
Chi-restraints excluded: chain C residue  278 CYS
Chi-restraints excluded: chain C residue  314 VAL
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  330 THR
Chi-restraints excluded: chain C residue  335 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 70 optimal weight:    8.9990
   chunk 42 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 89 optimal weight:    0.3980
   chunk 66 optimal weight:    8.9990
   chunk 77 optimal weight:    0.6980
   chunk 75 optimal weight:    7.9990
   chunk 98 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
B 219 ASN
** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.123671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.105886 restraints weight = 13841.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.109666 restraints weight = 6840.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.112229 restraints weight = 4163.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7856  Z= 0.193
  Angle     :  0.590  10.414  10704  Z= 0.310
  Chirality :  0.044   0.260   1218
  Planarity :  0.004   0.076   1397
  Dihedral  :  5.473  42.419   1084
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.47 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 19.53 %
    Favored  : 75.37 %
  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: -3.36 (0.24), residues: 1003
  helix: -2.92 (0.56), residues: 61
  sheet: -1.34 (0.45), residues: 144
  loop : -2.58 (0.20), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 242 
 HIS   0.002   0.001   HIS C 170 
 PHE   0.019   0.001   PHE B  48 
 TYR   0.022   0.002   TYR C 280 
 ARG   0.002   0.000   ARG C  92 

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 185
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 ASP cc_start: 0.7432 (m-30) cc_final: 0.7124 (p0)
REVERT: A   56 LYS cc_start: 0.8530 (tttm) cc_final: 0.8230 (tppt)
REVERT: A   80 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8174 (m)
REVERT: A   97 MET cc_start: 0.8148 (mtp) cc_final: 0.7833 (mtt)
REVERT: A  124 ASN cc_start: 0.8967 (m110) cc_final: 0.8517 (m110)
REVERT: A  182 MET cc_start: 0.8339 (mmt) cc_final: 0.8054 (mmt)
REVERT: A  213 LEU cc_start: 0.9197 (pt) cc_final: 0.8505 (pp)
REVERT: A  318 PHE cc_start: 0.8612 (t80) cc_final: 0.8025 (t80)
REVERT: A  329 TYR cc_start: 0.8472 (t80) cc_final: 0.8121 (t80)
REVERT: B  195 GLU cc_start: 0.8204 (tp30) cc_final: 0.7920 (tp30)
REVERT: B  256 GLN cc_start: 0.9007 (mm110) cc_final: 0.8706 (mm-40)
REVERT: B  262 GLU cc_start: 0.8072 (tp30) cc_final: 0.7823 (mm-30)
REVERT: B  329 TYR cc_start: 0.9019 (t80) cc_final: 0.8530 (t80)
REVERT: B  348 THR cc_start: 0.8530 (m) cc_final: 0.8298 (p)
REVERT: B  354 ASN cc_start: 0.8251 (t0) cc_final: 0.7996 (t0)
REVERT: C   53 ASP cc_start: 0.8824 (m-30) cc_final: 0.7867 (t0)
REVERT: C   83 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6783 (mm-30)
REVERT: C   91 GLN cc_start: 0.7197 (tp-100) cc_final: 0.6821 (tp-100)
REVERT: C   92 ARG cc_start: 0.7750 (mmt-90) cc_final: 0.7216 (mmt-90)
REVERT: C  245 ARG cc_start: 0.8254 (mtt90) cc_final: 0.8022 (mtt90)
  outliers start: 41
  outliers final: 32
  residues processed: 201
  average time/residue: 0.1523
  time to fit residues: 44.1442
Evaluate side-chains
  204 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 171
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  361 GLU
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  148 ILE
Chi-restraints excluded: chain C residue  161 ASN
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain C residue  240 VAL
Chi-restraints excluded: chain C residue  276 ILE
Chi-restraints excluded: chain C residue  278 CYS
Chi-restraints excluded: chain C residue  314 VAL
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  330 THR
Chi-restraints excluded: chain C residue  335 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 80 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9980
   chunk 91 optimal weight:    4.9990
   chunk 60 optimal weight:   10.0000
   chunk 65 optimal weight:    6.9990
   chunk 26 optimal weight:    0.0070
   chunk 52 optimal weight:    8.9990
   chunk 76 optimal weight:    7.9990
   chunk 36 optimal weight:    8.9990
   chunk 59 optimal weight:    4.9990
   chunk 90 optimal weight:    4.9990
   overall best weight:    3.2004

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

Flipped N/Q/H residues before XYZ refinement:
B  78 ASN
** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 219 ASN
** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.121422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.103542 restraints weight = 13763.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.107222 restraints weight = 6928.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.109727 restraints weight = 4287.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   7856  Z= 0.314
  Angle     :  0.656  11.207  10704  Z= 0.347
  Chirality :  0.046   0.274   1218
  Planarity :  0.004   0.082   1397
  Dihedral  :  5.791  36.772   1084
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.66 %
    Favored  : 87.34 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 21.14 %
    Favored  : 73.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.38 (0.24), residues: 1003
  helix: -2.70 (0.58), residues: 61
  sheet: -1.46 (0.45), residues: 144
  loop : -2.60 (0.20), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 242 
 HIS   0.004   0.001   HIS C 170 
 PHE   0.025   0.002   PHE C 192 
 TYR   0.022   0.002   TYR B 198 
 ARG   0.002   0.000   ARG C  92 

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 173
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 ASP cc_start: 0.7478 (m-30) cc_final: 0.7173 (p0)
REVERT: A   56 LYS cc_start: 0.8542 (tttm) cc_final: 0.8278 (tppt)
REVERT: A   80 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8351 (m)
REVERT: A   97 MET cc_start: 0.8175 (mtp) cc_final: 0.7858 (mtt)
REVERT: A  124 ASN cc_start: 0.9033 (m110) cc_final: 0.8662 (m110)
REVERT: A  213 LEU cc_start: 0.9285 (pt) cc_final: 0.8528 (pp)
REVERT: A  318 PHE cc_start: 0.8736 (t80) cc_final: 0.8201 (t80)
REVERT: A  329 TYR cc_start: 0.8522 (t80) cc_final: 0.8217 (t80)
REVERT: B  195 GLU cc_start: 0.8309 (tp30) cc_final: 0.8000 (tp30)
REVERT: B  262 GLU cc_start: 0.8123 (tp30) cc_final: 0.7830 (mm-30)
REVERT: B  329 TYR cc_start: 0.9028 (t80) cc_final: 0.8582 (t80)
REVERT: B  348 THR cc_start: 0.8651 (m) cc_final: 0.8400 (p)
REVERT: B  354 ASN cc_start: 0.8323 (t0) cc_final: 0.8024 (t0)
REVERT: C   53 ASP cc_start: 0.9018 (m-30) cc_final: 0.8185 (t0)
REVERT: C   83 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6964 (mm-30)
REVERT: C   91 GLN cc_start: 0.7306 (tp-100) cc_final: 0.6912 (tp-100)
REVERT: C  131 ILE cc_start: 0.9206 (mt) cc_final: 0.8963 (mm)
  outliers start: 40
  outliers final: 34
  residues processed: 191
  average time/residue: 0.1436
  time to fit residues: 40.9284
Evaluate side-chains
  203 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 168
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  361 GLU
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  161 ASN
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain C residue  240 VAL
Chi-restraints excluded: chain C residue  276 ILE
Chi-restraints excluded: chain C residue  278 CYS
Chi-restraints excluded: chain C residue  314 VAL
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  330 THR
Chi-restraints excluded: chain C residue  335 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 34 optimal weight:    8.9990
   chunk 48 optimal weight:    0.0980
   chunk 18 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 75 optimal weight:    9.9990
   chunk 81 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0020
   chunk 57 optimal weight:    6.9990
   chunk 36 optimal weight:    0.0270
   chunk 20 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.6048

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

Flipped N/Q/H residues before XYZ refinement:
A 357 ASN
B 219 ASN
B 317 ASN
** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.127489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.109062 restraints weight = 13806.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.112926 restraints weight = 6936.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.115491 restraints weight = 4273.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   7856  Z= 0.155
  Angle     :  0.592   8.810  10704  Z= 0.310
  Chirality :  0.044   0.241   1218
  Planarity :  0.004   0.079   1397
  Dihedral  :  5.272  36.341   1084
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 23.26 %
    Favored  : 72.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.17 (0.25), residues: 1003
  helix: -2.41 (0.62), residues: 61
  sheet: -1.55 (0.44), residues: 154
  loop : -2.40 (0.21), residues: 788

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C 242 
 HIS   0.002   0.000   HIS A 158 
 PHE   0.025   0.002   PHE C 192 
 TYR   0.018   0.001   TYR B 198 
 ARG   0.002   0.000   ARG C  92 

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 188
  time to evaluate  : 0.859 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 ASP cc_start: 0.7499 (m-30) cc_final: 0.7223 (p0)
REVERT: A   56 LYS cc_start: 0.8570 (tttm) cc_final: 0.8264 (tppt)
REVERT: A   80 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8140 (m)
REVERT: A   97 MET cc_start: 0.8082 (mtp) cc_final: 0.7759 (mtt)
REVERT: A  124 ASN cc_start: 0.8892 (m110) cc_final: 0.8572 (m110)
REVERT: A  213 LEU cc_start: 0.9067 (pt) cc_final: 0.8420 (pp)
REVERT: A  258 PHE cc_start: 0.8389 (m-10) cc_final: 0.7270 (m-10)
REVERT: A  318 PHE cc_start: 0.8567 (t80) cc_final: 0.7965 (t80)
REVERT: A  329 TYR cc_start: 0.8537 (t80) cc_final: 0.8294 (t80)
REVERT: A  336 GLU cc_start: 0.8292 (pt0) cc_final: 0.8029 (pt0)
REVERT: B   92 ARG cc_start: 0.8081 (mpt180) cc_final: 0.7631 (mmt-90)
REVERT: B  195 GLU cc_start: 0.8179 (tp30) cc_final: 0.7911 (tp30)
REVERT: B  262 GLU cc_start: 0.8146 (tp30) cc_final: 0.7912 (mm-30)
REVERT: B  329 TYR cc_start: 0.9058 (t80) cc_final: 0.8691 (t80)
REVERT: B  348 THR cc_start: 0.8498 (m) cc_final: 0.8267 (p)
REVERT: B  354 ASN cc_start: 0.8195 (t0) cc_final: 0.7946 (t0)
REVERT: C   53 ASP cc_start: 0.8904 (m-30) cc_final: 0.7944 (t0)
REVERT: C   83 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6830 (mm-30)
REVERT: C   91 GLN cc_start: 0.7191 (tp-100) cc_final: 0.6806 (tp-100)
  outliers start: 32
  outliers final: 24
  residues processed: 205
  average time/residue: 0.1400
  time to fit residues: 42.1757
Evaluate side-chains
  201 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 176
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  148 ILE
Chi-restraints excluded: chain C residue  161 ASN
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain C residue  240 VAL
Chi-restraints excluded: chain C residue  276 ILE
Chi-restraints excluded: chain C residue  314 VAL
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  330 THR
Chi-restraints excluded: chain C residue  335 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   chunk 12 optimal weight:    8.9990
   chunk 23 optimal weight:    1.9990
   chunk 75 optimal weight:    8.9990
   chunk 31 optimal weight:   10.0000
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
B 219 ASN
B 317 ASN
** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.124824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.106649 restraints weight = 13957.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.110432 restraints weight = 6995.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.113022 restraints weight = 4300.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7856  Z= 0.228
  Angle     :  0.613  10.754  10704  Z= 0.324
  Chirality :  0.044   0.268   1218
  Planarity :  0.003   0.046   1397
  Dihedral  :  5.259  31.334   1083
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.07 %
    Favored  : 89.93 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 24.13 %
    Favored  : 71.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.17 (0.25), residues: 1003
  helix: -2.26 (0.62), residues: 61
  sheet: -1.61 (0.43), residues: 154
  loop : -2.41 (0.21), residues: 788

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 242 
 HIS   0.002   0.001   HIS C 170 
 PHE   0.037   0.002   PHE C 192 
 TYR   0.021   0.002   TYR B 198 
 ARG   0.006   0.000   ARG C  92 

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 171
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.8530 (tttm) cc_final: 0.8236 (tppt)
REVERT: A   80 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8286 (m)
REVERT: A   97 MET cc_start: 0.8169 (mtp) cc_final: 0.7842 (mtt)
REVERT: A  124 ASN cc_start: 0.9034 (m110) cc_final: 0.8541 (m110)
REVERT: A  135 GLU cc_start: 0.8049 (pm20) cc_final: 0.7829 (pt0)
REVERT: A  213 LEU cc_start: 0.9256 (pt) cc_final: 0.8577 (pp)
REVERT: A  318 PHE cc_start: 0.8647 (t80) cc_final: 0.8066 (t80)
REVERT: A  329 TYR cc_start: 0.8572 (t80) cc_final: 0.8350 (t80)
REVERT: A  336 GLU cc_start: 0.8310 (pt0) cc_final: 0.7946 (pt0)
REVERT: B   92 ARG cc_start: 0.8130 (mpt180) cc_final: 0.7699 (mmt-90)
REVERT: B   97 MET cc_start: 0.8993 (mtp) cc_final: 0.8734 (mtm)
REVERT: B  195 GLU cc_start: 0.8314 (tp30) cc_final: 0.8013 (tp30)
REVERT: B  262 GLU cc_start: 0.8130 (tp30) cc_final: 0.7868 (mm-30)
REVERT: B  329 TYR cc_start: 0.9066 (t80) cc_final: 0.8697 (t80)
REVERT: B  348 THR cc_start: 0.8574 (m) cc_final: 0.8351 (p)
REVERT: B  354 ASN cc_start: 0.8279 (t0) cc_final: 0.7987 (t0)
REVERT: C   53 ASP cc_start: 0.8954 (m-30) cc_final: 0.8164 (t0)
REVERT: C   83 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6845 (mm-30)
REVERT: C   91 GLN cc_start: 0.7286 (tp-100) cc_final: 0.6897 (tp-100)
REVERT: C   92 ARG cc_start: 0.7701 (mmt-90) cc_final: 0.7064 (mmt-90)
REVERT: C  131 ILE cc_start: 0.9190 (mt) cc_final: 0.8960 (mm)
  outliers start: 37
  outliers final: 31
  residues processed: 192
  average time/residue: 0.1446
  time to fit residues: 41.2843
Evaluate side-chains
  199 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 167
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  361 GLU
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  229 ASN
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  161 ASN
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain C residue  240 VAL
Chi-restraints excluded: chain C residue  276 ILE
Chi-restraints excluded: chain C residue  314 VAL
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  330 THR
Chi-restraints excluded: chain C residue  335 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 73 optimal weight:    5.9990
   chunk 55 optimal weight:    7.9990
   chunk 25 optimal weight:    8.9990
   chunk 43 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 85 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 91 optimal weight:    0.0570
   chunk 8 optimal weight:    9.9990
   chunk 92 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   overall best weight:    2.8106

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

Flipped N/Q/H residues before XYZ refinement:
A 205 GLN
B 219 ASN
C 146 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.122759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.104720 restraints weight = 14070.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.108467 restraints weight = 7008.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.111009 restraints weight = 4308.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7856  Z= 0.288
  Angle     :  0.645  10.673  10704  Z= 0.342
  Chirality :  0.045   0.265   1218
  Planarity :  0.004   0.052   1397
  Dihedral  :  5.466  24.802   1083
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.07 %
    Favored  : 88.93 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 23.51 %
    Favored  : 71.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.21 (0.25), residues: 1003
  helix: -2.16 (0.66), residues: 55
  sheet: -1.67 (0.43), residues: 154
  loop : -2.44 (0.21), residues: 794

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 242 
 HIS   0.003   0.001   HIS C 170 
 PHE   0.019   0.002   PHE C 192 
 TYR   0.023   0.002   TYR B 198 
 ARG   0.004   0.001   ARG C  92 

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 172
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.8540 (tttm) cc_final: 0.8247 (tppt)
REVERT: A   80 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8345 (m)
REVERT: A   97 MET cc_start: 0.8280 (mtp) cc_final: 0.7962 (mtt)
REVERT: A  124 ASN cc_start: 0.9083 (m110) cc_final: 0.8650 (m110)
REVERT: A  228 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.8004 (p90)
REVERT: A  258 PHE cc_start: 0.8316 (m-10) cc_final: 0.7843 (m-10)
REVERT: A  318 PHE cc_start: 0.8769 (t80) cc_final: 0.8194 (t80)
REVERT: A  329 TYR cc_start: 0.8569 (t80) cc_final: 0.8344 (t80)
REVERT: B  195 GLU cc_start: 0.8352 (tp30) cc_final: 0.8053 (tp30)
REVERT: B  262 GLU cc_start: 0.8122 (tp30) cc_final: 0.7835 (mm-30)
REVERT: B  329 TYR cc_start: 0.9057 (t80) cc_final: 0.8609 (t80)
REVERT: B  348 THR cc_start: 0.8605 (m) cc_final: 0.8392 (p)
REVERT: B  354 ASN cc_start: 0.8314 (t0) cc_final: 0.8034 (t0)
REVERT: C   53 ASP cc_start: 0.9053 (m-30) cc_final: 0.8210 (t0)
REVERT: C   83 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6955 (mm-30)
REVERT: C   91 GLN cc_start: 0.7364 (tp-100) cc_final: 0.6975 (tp-100)
REVERT: C  131 ILE cc_start: 0.9185 (mt) cc_final: 0.8947 (mm)
  outliers start: 40
  outliers final: 33
  residues processed: 193
  average time/residue: 0.1341
  time to fit residues: 38.3598
Evaluate side-chains
  204 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 169
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  205 GLN
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  228 PHE
Chi-restraints excluded: chain A residue  361 GLU
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  229 ASN
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  161 ASN
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain C residue  240 VAL
Chi-restraints excluded: chain C residue  276 ILE
Chi-restraints excluded: chain C residue  314 VAL
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  330 THR
Chi-restraints excluded: chain C residue  335 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 37 optimal weight:    6.9990
   chunk 91 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0000
   chunk 56 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   chunk 44 optimal weight:    9.9990
   chunk 25 optimal weight:    6.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 219 ASN
** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.124725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.106488 restraints weight = 13984.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.110280 restraints weight = 7015.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.112866 restraints weight = 4330.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7856  Z= 0.215
  Angle     :  0.619  10.293  10704  Z= 0.328
  Chirality :  0.045   0.267   1218
  Planarity :  0.004   0.054   1397
  Dihedral  :  5.314  25.278   1083
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.57 %
    Favored  : 90.43 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 23.88 %
    Favored  : 71.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.12 (0.25), residues: 1003
  helix: -2.03 (0.67), residues: 55
  sheet: -1.59 (0.43), residues: 154
  loop : -2.38 (0.21), residues: 794

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 242 
 HIS   0.002   0.001   HIS C 170 
 PHE   0.013   0.001   PHE B 318 
 TYR   0.022   0.002   TYR B 198 
 ARG   0.006   0.001   ARG C  92 

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 169
  time to evaluate  : 0.798 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.8533 (tttm) cc_final: 0.8251 (tppt)
REVERT: A   80 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8299 (m)
REVERT: A   97 MET cc_start: 0.8264 (mtp) cc_final: 0.7937 (mtt)
REVERT: A  103 MET cc_start: 0.8808 (ttm) cc_final: 0.8583 (ttm)
REVERT: A  124 ASN cc_start: 0.9066 (m110) cc_final: 0.8533 (m110)
REVERT: A  213 LEU cc_start: 0.9174 (pt) cc_final: 0.8516 (pp)
REVERT: A  228 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.7935 (p90)
REVERT: A  258 PHE cc_start: 0.8301 (m-10) cc_final: 0.7764 (m-10)
REVERT: A  318 PHE cc_start: 0.8696 (t80) cc_final: 0.8088 (t80)
REVERT: A  329 TYR cc_start: 0.8575 (t80) cc_final: 0.8360 (t80)
REVERT: B   92 ARG cc_start: 0.8193 (mpt180) cc_final: 0.7991 (mmt180)
REVERT: B  195 GLU cc_start: 0.8219 (tp30) cc_final: 0.7937 (tp30)
REVERT: B  262 GLU cc_start: 0.8166 (tp30) cc_final: 0.7910 (mm-30)
REVERT: B  329 TYR cc_start: 0.9058 (t80) cc_final: 0.8710 (t80)
REVERT: B  354 ASN cc_start: 0.8270 (t0) cc_final: 0.7990 (t0)
REVERT: C   53 ASP cc_start: 0.9047 (m-30) cc_final: 0.8219 (t0)
REVERT: C   83 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6946 (mm-30)
REVERT: C   91 GLN cc_start: 0.7394 (tp-100) cc_final: 0.7025 (tp-100)
REVERT: C   92 ARG cc_start: 0.7612 (mmt-90) cc_final: 0.7055 (mmt-90)
REVERT: C  131 ILE cc_start: 0.9148 (mt) cc_final: 0.8915 (mm)
  outliers start: 35
  outliers final: 30
  residues processed: 188
  average time/residue: 0.1355
  time to fit residues: 37.5466
Evaluate side-chains
  201 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 169
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  228 PHE
Chi-restraints excluded: chain A residue  361 GLU
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  229 ASN
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  161 ASN
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain C residue  240 VAL
Chi-restraints excluded: chain C residue  276 ILE
Chi-restraints excluded: chain C residue  314 VAL
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  330 THR
Chi-restraints excluded: chain C residue  335 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 16 optimal weight:    8.9990
   chunk 31 optimal weight:   10.0000
   chunk 48 optimal weight:    9.9990
   chunk 77 optimal weight:    0.0070
   chunk 76 optimal weight:    0.2980
   chunk 40 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 17 optimal weight:    7.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    1.4002

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

Flipped N/Q/H residues before XYZ refinement:
A 205 GLN
B 219 ASN
** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.122396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.104337 restraints weight = 14128.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.108099 restraints weight = 6963.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.110665 restraints weight = 4242.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.2443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7856  Z= 0.190
  Angle     :  0.607   9.992  10704  Z= 0.318
  Chirality :  0.044   0.263   1218
  Planarity :  0.003   0.052   1397
  Dihedral  :  5.290  47.188   1083
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.87 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 24.13 %
    Favored  : 71.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.04 (0.25), residues: 1003
  helix: -1.89 (0.69), residues: 55
  sheet: -1.53 (0.43), residues: 154
  loop : -2.34 (0.21), residues: 794

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 242 
 HIS   0.001   0.000   HIS C 170 
 PHE   0.013   0.001   PHE C  48 
 TYR   0.021   0.001   TYR B 198 
 ARG   0.005   0.000   ARG C  92 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2665.31 seconds
wall clock time: 48 minutes 32.11 seconds (2912.11 seconds total)