Starting phenix.real_space_refine
on Tue Mar  3 18:04:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6kmf_0724/03_2026/6kmf_0724.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6kmf_0724/03_2026/6kmf_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_0724/03_2026/6kmf_0724.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6kmf_0724/03_2026/6kmf_0724.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6kmf_0724/03_2026/6kmf_0724.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6kmf_0724/03_2026/6kmf_0724.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.71, per 1000 atoms: 0.22
  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: 0.69
  Conformation dependent library (CDL) restraints added in 220.4 milliseconds
  

  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: 0.28
  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: 1.18

  Time building geometry restraints manager: 0.87 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:             4.180
  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:          0.130
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     8.130
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.840
-------------------------------------------------------------------------------
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= 0.261
  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 : 5.25
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -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
 ARG   0.003   0.001   ARG A 172 
 TYR   0.030   0.003   TYR C 150 
 PHE   0.011   0.002   PHE B 318 
 TRP   0.019   0.002   TRP A 242 
 HIS   0.003   0.001   HIS B 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00578 ( 7856)
  covalent geometry    : angle       0.90095 (10704)
  hydrogen bonds       : bond        0.21109 (  111)
  hydrogen bonds       : angle       8.41591 (  327)

*********************** 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  : 0.250 
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: 0.8098 (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: 0.8711 (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: 0.0747
  time to fit residues: 23.6666
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  : 0.283 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.4980
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0670
   overall best weight:    1.1124

-------------------------------------------------------------------------------
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 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 219 ASN
B 286 ASN
C 236 ASN
C 286 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.125170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.107372 restraints weight = 13707.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.111072 restraints weight = 6992.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.113610 restraints weight = 4328.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.115393 restraints weight = 3011.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.116670 restraints weight = 2269.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.1466

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= 0.116
  Angle     :  0.598   9.136  10704  Z= 0.319
  Chirality :  0.044   0.246   1218
  Planarity :  0.004   0.074   1397
  Dihedral  :  5.886  53.478   1084
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.37 %
    Favored  : 90.63 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 18.03 %
    Favored  : 78.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.86 (0.23), residues: 1003
  helix: -4.20 (0.42), residues: 54
  sheet: -1.45 (0.45), residues: 144
  loop : -2.94 (0.19), residues: 805

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  92 
 TYR   0.019   0.001   TYR B 198 
 PHE   0.010   0.001   PHE C  48 
 TRP   0.017   0.001   TRP A 242 
 HIS   0.002   0.001   HIS A 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 7856)
  covalent geometry    : angle       0.59836 (10704)
  hydrogen bonds       : bond        0.03584 (  111)
  hydrogen bonds       : angle       6.16751 (  327)

*********************** 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
  237 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 207
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.7000 (p0)
REVERT: A   56 LYS cc_start: 0.8469 (tttm) cc_final: 0.8183 (tppt)
REVERT: A   80 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8101 (m)
REVERT: A   97 MET cc_start: 0.8210 (mtp) cc_final: 0.7905 (mtt)
REVERT: A  124 ASN cc_start: 0.9013 (m110) cc_final: 0.8607 (m110)
REVERT: A  182 MET cc_start: 0.8289 (mmt) cc_final: 0.7967 (mmt)
REVERT: A  213 LEU cc_start: 0.9091 (pt) cc_final: 0.8640 (pp)
REVERT: A  258 PHE cc_start: 0.8756 (m-80) cc_final: 0.8069 (m-80)
REVERT: A  318 PHE cc_start: 0.8459 (t80) cc_final: 0.7906 (t80)
REVERT: B  195 GLU cc_start: 0.8202 (tp30) cc_final: 0.7936 (tp30)
REVERT: B  256 GLN cc_start: 0.9012 (mm110) cc_final: 0.8715 (mm-40)
REVERT: B  317 ASN cc_start: 0.8160 (t0) cc_final: 0.7947 (t0)
REVERT: B  329 TYR cc_start: 0.8981 (t80) cc_final: 0.8578 (t80)
REVERT: B  348 THR cc_start: 0.8606 (m) cc_final: 0.8378 (p)
REVERT: B  354 ASN cc_start: 0.8141 (t0) cc_final: 0.7918 (t0)
REVERT: C   53 ASP cc_start: 0.8226 (m-30) cc_final: 0.7844 (t0)
REVERT: C   83 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6827 (mm-30)
REVERT: D  368 GLN cc_start: 0.7294 (tm-30) cc_final: 0.6837 (tm-30)
  outliers start: 30
  outliers final: 18
  residues processed: 223
  average time/residue: 0.0581
  time to fit residues: 19.5710
Evaluate side-chains
  203 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 183
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
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 58 optimal weight:    1.9990
   chunk 7 optimal weight:    9.9990
   chunk 14 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 67 optimal weight:    0.0870
   chunk 13 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 91 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    2.0166

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

Flipped N/Q/H residues before XYZ refinement:
A 333 ASN
B 157 ASN
B 219 ASN
C  78 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 = 0.3497 r_free = 0.3497 target = 0.124323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.106502 restraints weight = 13715.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.110268 restraints weight = 6797.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.112844 restraints weight = 4148.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.114667 restraints weight = 2865.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.115921 restraints weight = 2139.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.1668

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= 0.147
  Angle     :  0.611   9.688  10704  Z= 0.322
  Chirality :  0.044   0.260   1218
  Planarity :  0.004   0.076   1397
  Dihedral  :  5.661  47.933   1084
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.97 %
    Favored  : 90.03 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 17.91 %
    Favored  : 76.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.67 (0.23), residues: 1003
  helix: -3.66 (0.45), residues: 61
  sheet: -1.42 (0.45), residues: 144
  loop : -2.79 (0.19), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  92 
 TYR   0.022   0.002   TYR B 198 
 PHE   0.019   0.002   PHE C 192 
 TRP   0.017   0.001   TRP A 242 
 HIS   0.003   0.001   HIS A 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 7856)
  covalent geometry    : angle       0.61117 (10704)
  hydrogen bonds       : bond        0.03487 (  111)
  hydrogen bonds       : angle       5.88359 (  327)

*********************** 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
  230 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 188
  time to evaluate  : 0.277 
Fit side-chains
REVERT: A   53 ASP cc_start: 0.7471 (m-30) cc_final: 0.7049 (p0)
REVERT: A   56 LYS cc_start: 0.8470 (tttm) cc_final: 0.8214 (tppt)
REVERT: A   80 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.8152 (m)
REVERT: A   97 MET cc_start: 0.8208 (mtp) cc_final: 0.7905 (mtt)
REVERT: A  124 ASN cc_start: 0.9109 (m110) cc_final: 0.8636 (m110)
REVERT: A  182 MET cc_start: 0.8343 (mmt) cc_final: 0.8040 (mmt)
REVERT: A  213 LEU cc_start: 0.9229 (pt) cc_final: 0.8620 (pp)
REVERT: A  258 PHE cc_start: 0.8718 (m-80) cc_final: 0.7995 (m-80)
REVERT: A  318 PHE cc_start: 0.8587 (t80) cc_final: 0.8033 (t80)
REVERT: A  329 TYR cc_start: 0.8376 (t80) cc_final: 0.7960 (t80)
REVERT: B  195 GLU cc_start: 0.8126 (tp30) cc_final: 0.7848 (tp30)
REVERT: B  256 GLN cc_start: 0.9004 (mm110) cc_final: 0.8701 (mm-40)
REVERT: B  317 ASN cc_start: 0.8206 (t0) cc_final: 0.7899 (t0)
REVERT: B  329 TYR cc_start: 0.8988 (t80) cc_final: 0.8550 (t80)
REVERT: B  348 THR cc_start: 0.8597 (m) cc_final: 0.8355 (p)
REVERT: B  354 ASN cc_start: 0.8204 (t0) cc_final: 0.7970 (t0)
REVERT: C   53 ASP cc_start: 0.8375 (m-30) cc_final: 0.7841 (t0)
REVERT: C   83 GLU cc_start: 0.7269 (mm-30) cc_final: 0.6855 (mm-30)
REVERT: C  146 ASN cc_start: 0.7149 (OUTLIER) cc_final: 0.6926 (p0)
REVERT: D  368 GLN cc_start: 0.7394 (tm-30) cc_final: 0.6881 (tm-30)
  outliers start: 42
  outliers final: 31
  residues processed: 209
  average time/residue: 0.0591
  time to fit residues: 18.5224
Evaluate side-chains
  205 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 172
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
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  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
Chi-restraints excluded: chain C residue  359 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 44 optimal weight:    6.9990
   chunk 55 optimal weight:    0.0000
   chunk 92 optimal weight:    5.9990
   chunk 83 optimal weight:    2.9990
   chunk 86 optimal weight:    7.9990
   chunk 26 optimal weight:    3.9990
   chunk 12 optimal weight:   10.0000
   chunk 52 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 84 optimal weight:    0.3980
   chunk 53 optimal weight:    7.9990
   overall best weight:    1.8790

-------------------------------------------------------------------------------
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 146 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.123109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.105210 restraints weight = 14005.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.109008 restraints weight = 6874.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.111585 restraints weight = 4180.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.113411 restraints weight = 2879.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.114700 restraints weight = 2148.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.1822

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= 0.139
  Angle     :  0.597  10.219  10704  Z= 0.316
  Chirality :  0.044   0.258   1218
  Planarity :  0.004   0.078   1397
  Dihedral  :  5.599  44.970   1084
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.67 %
    Favored  : 90.33 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 18.66 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.50 (0.24), residues: 1003
  helix: -3.27 (0.51), residues: 61
  sheet: -1.41 (0.45), residues: 144
  loop : -2.67 (0.20), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 245 
 TYR   0.021   0.002   TYR C 280 
 PHE   0.021   0.002   PHE C 192 
 TRP   0.015   0.001   TRP A 242 
 HIS   0.003   0.001   HIS A 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 7856)
  covalent geometry    : angle       0.59738 (10704)
  hydrogen bonds       : bond        0.03362 (  111)
  hydrogen bonds       : angle       5.70000 (  327)

*********************** 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
  223 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 185
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 ASP cc_start: 0.7433 (m-30) cc_final: 0.7124 (p0)
REVERT: A   56 LYS cc_start: 0.8522 (tttm) cc_final: 0.8224 (tppt)
REVERT: A   80 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8130 (m)
REVERT: A   97 MET cc_start: 0.8131 (mtp) cc_final: 0.7812 (mtt)
REVERT: A  124 ASN cc_start: 0.8985 (m110) cc_final: 0.8530 (m110)
REVERT: A  182 MET cc_start: 0.8336 (mmt) cc_final: 0.8059 (mmt)
REVERT: A  213 LEU cc_start: 0.9197 (pt) cc_final: 0.8563 (pp)
REVERT: A  318 PHE cc_start: 0.8608 (t80) cc_final: 0.7996 (t80)
REVERT: A  329 TYR cc_start: 0.8383 (t80) cc_final: 0.7988 (t80)
REVERT: B  195 GLU cc_start: 0.8268 (tp30) cc_final: 0.7989 (tp30)
REVERT: B  256 GLN cc_start: 0.9011 (mm110) cc_final: 0.8710 (mm-40)
REVERT: B  262 GLU cc_start: 0.8109 (tp30) cc_final: 0.7828 (mm-30)
REVERT: B  317 ASN cc_start: 0.8209 (t0) cc_final: 0.7982 (t0)
REVERT: B  329 TYR cc_start: 0.9001 (t80) cc_final: 0.8542 (t80)
REVERT: B  348 THR cc_start: 0.8582 (m) cc_final: 0.8335 (p)
REVERT: B  354 ASN cc_start: 0.8181 (t0) cc_final: 0.7941 (t0)
REVERT: C   53 ASP cc_start: 0.8441 (m-30) cc_final: 0.7865 (t0)
REVERT: C   83 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6806 (mm-30)
REVERT: C   91 GLN cc_start: 0.7187 (tp-100) cc_final: 0.6796 (tp-100)
  outliers start: 38
  outliers final: 31
  residues processed: 201
  average time/residue: 0.0585
  time to fit residues: 17.6251
Evaluate side-chains
  206 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 174
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
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  248 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  148 ILE
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain C residue  240 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 77 optimal weight:    0.0060
   chunk 5 optimal weight:    1.9990
   chunk 70 optimal weight:    8.9990
   chunk 24 optimal weight:    7.9990
   chunk 34 optimal weight:   10.0000
   chunk 88 optimal weight:    0.0060
   chunk 40 optimal weight:   10.0000
   chunk 43 optimal weight:    7.9990
   chunk 79 optimal weight:    8.9990
   chunk 8 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.1416

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.125131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.107533 restraints weight = 13954.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.111220 restraints weight = 7096.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.113755 restraints weight = 4376.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.115517 restraints weight = 3034.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.116826 restraints weight = 2281.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.2019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7856  Z= 0.109
  Angle     :  0.574  10.515  10704  Z= 0.301
  Chirality :  0.044   0.271   1218
  Planarity :  0.004   0.077   1397
  Dihedral  :  5.305  41.578   1084
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.47 %
    Favored  : 91.53 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 19.78 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.33 (0.24), residues: 1003
  helix: -2.89 (0.57), residues: 61
  sheet: -1.59 (0.43), residues: 154
  loop : -2.51 (0.20), residues: 788

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  92 
 TYR   0.022   0.001   TYR C 280 
 PHE   0.020   0.001   PHE B  48 
 TRP   0.015   0.001   TRP A 242 
 HIS   0.001   0.000   HIS C 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 7856)
  covalent geometry    : angle       0.57373 (10704)
  hydrogen bonds       : bond        0.03034 (  111)
  hydrogen bonds       : angle       5.49551 (  327)

*********************** 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
  231 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 192
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A   53 ASP cc_start: 0.7472 (m-30) cc_final: 0.7181 (p0)
REVERT: A   56 LYS cc_start: 0.8510 (tttm) cc_final: 0.8219 (tppt)
REVERT: A   80 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8117 (m)
REVERT: A   97 MET cc_start: 0.8106 (mtp) cc_final: 0.7786 (mtt)
REVERT: A  124 ASN cc_start: 0.8908 (m110) cc_final: 0.8523 (m110)
REVERT: A  182 MET cc_start: 0.8312 (mmt) cc_final: 0.8053 (mmt)
REVERT: A  213 LEU cc_start: 0.9079 (pt) cc_final: 0.8432 (pp)
REVERT: A  318 PHE cc_start: 0.8577 (t80) cc_final: 0.7991 (t80)
REVERT: A  329 TYR cc_start: 0.8428 (t80) cc_final: 0.8115 (t80)
REVERT: A  336 GLU cc_start: 0.8258 (pt0) cc_final: 0.7917 (pt0)
REVERT: B   92 ARG cc_start: 0.8165 (mpt180) cc_final: 0.7865 (mpt180)
REVERT: B  195 GLU cc_start: 0.8255 (tp30) cc_final: 0.8006 (tp30)
REVERT: B  256 GLN cc_start: 0.9020 (mm110) cc_final: 0.8665 (mm-40)
REVERT: B  262 GLU cc_start: 0.8113 (tp30) cc_final: 0.7870 (mm-30)
REVERT: B  329 TYR cc_start: 0.9007 (t80) cc_final: 0.8627 (t80)
REVERT: B  341 TYR cc_start: 0.7828 (m-80) cc_final: 0.7594 (m-80)
REVERT: B  348 THR cc_start: 0.8498 (m) cc_final: 0.8270 (p)
REVERT: B  354 ASN cc_start: 0.8215 (t0) cc_final: 0.7946 (t0)
REVERT: C   53 ASP cc_start: 0.8451 (m-30) cc_final: 0.7839 (t0)
REVERT: C   83 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6753 (mm-30)
REVERT: C   92 ARG cc_start: 0.7606 (mmt-90) cc_final: 0.7311 (mmt-90)
  outliers start: 39
  outliers final: 28
  residues processed: 211
  average time/residue: 0.0628
  time to fit residues: 19.7470
Evaluate side-chains
  212 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 183
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
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  221 LEU
Chi-restraints excluded: chain A residue  248 VAL
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  182 MET
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  221 LEU
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  121 THR
Chi-restraints excluded: chain C residue  146 ASN
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 30 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 45 optimal weight:    8.9990
   chunk 81 optimal weight:    4.9990
   chunk 64 optimal weight:   10.0000
   overall best weight:    2.1588

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.123122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.105120 restraints weight = 14097.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.108872 restraints weight = 7016.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.111468 restraints weight = 4297.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.113304 restraints weight = 2966.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.114594 restraints weight = 2216.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.2081

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= 0.151
  Angle     :  0.604  10.564  10704  Z= 0.317
  Chirality :  0.044   0.262   1218
  Planarity :  0.004   0.081   1397
  Dihedral  :  5.319  36.968   1083
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.87 %
    Favored  : 89.13 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 21.02 %
    Favored  : 74.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.28 (0.24), residues: 1003
  helix: -2.60 (0.60), residues: 61
  sheet: -1.64 (0.43), residues: 154
  loop : -2.47 (0.20), residues: 788

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 245 
 TYR   0.021   0.002   TYR B 198 
 PHE   0.014   0.002   PHE C  48 
 TRP   0.020   0.001   TRP A 242 
 HIS   0.002   0.001   HIS C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 7856)
  covalent geometry    : angle       0.60420 (10704)
  hydrogen bonds       : bond        0.03278 (  111)
  hydrogen bonds       : angle       5.51795 (  327)

*********************** 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
  225 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 185
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A   53 ASP cc_start: 0.7477 (m-30) cc_final: 0.7248 (p0)
REVERT: A   56 LYS cc_start: 0.8518 (tttm) cc_final: 0.8223 (tppt)
REVERT: A   80 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8222 (m)
REVERT: A   97 MET cc_start: 0.8118 (mtp) cc_final: 0.7786 (mtt)
REVERT: A  124 ASN cc_start: 0.8930 (m110) cc_final: 0.8513 (m110)
REVERT: A  213 LEU cc_start: 0.9202 (pt) cc_final: 0.8542 (pp)
REVERT: A  222 THR cc_start: 0.7664 (m) cc_final: 0.7451 (m)
REVERT: A  318 PHE cc_start: 0.8636 (t80) cc_final: 0.8055 (t80)
REVERT: A  329 TYR cc_start: 0.8480 (t80) cc_final: 0.8193 (t80)
REVERT: B   91 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7899 (mm-40)
REVERT: B   92 ARG cc_start: 0.8190 (mpt180) cc_final: 0.7736 (mmt-90)
REVERT: B  195 GLU cc_start: 0.8277 (tp30) cc_final: 0.8016 (tp30)
REVERT: B  262 GLU cc_start: 0.8069 (tp30) cc_final: 0.7797 (mm-30)
REVERT: B  329 TYR cc_start: 0.9023 (t80) cc_final: 0.8665 (t80)
REVERT: B  348 THR cc_start: 0.8579 (m) cc_final: 0.8353 (p)
REVERT: B  354 ASN cc_start: 0.8242 (t0) cc_final: 0.7973 (t0)
REVERT: C   83 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6781 (mm-30)
REVERT: C   91 GLN cc_start: 0.7245 (tp-100) cc_final: 0.6854 (tp-100)
REVERT: C   92 ARG cc_start: 0.7785 (mmt-90) cc_final: 0.7264 (mmt-90)
REVERT: C  131 ILE cc_start: 0.9147 (mt) cc_final: 0.8887 (mm)
  outliers start: 40
  outliers final: 34
  residues processed: 203
  average time/residue: 0.0599
  time to fit residues: 18.5900
Evaluate side-chains
  212 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 177
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
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  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  221 LEU
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   94 LEU
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  161 ASN
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 95 optimal weight:    9.9990
   chunk 44 optimal weight:    0.0980
   chunk 64 optimal weight:   10.0000
   chunk 62 optimal weight:    0.3980
   chunk 71 optimal weight:   10.0000
   chunk 41 optimal weight:    5.9990
   chunk 21 optimal weight:    6.9990
   chunk 27 optimal weight:    6.9990
   chunk 20 optimal weight:    5.9990
   chunk 97 optimal weight:    9.9990
   overall best weight:    2.8986

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

Flipped N/Q/H residues before XYZ refinement:
B  78 ASN
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 = 0.3471 r_free = 0.3471 target = 0.122253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.104383 restraints weight = 13993.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.108111 restraints weight = 6930.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.110639 restraints weight = 4248.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.112452 restraints weight = 2945.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.113763 restraints weight = 2213.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.2072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   7856  Z= 0.191
  Angle     :  0.637  11.177  10704  Z= 0.335
  Chirality :  0.045   0.260   1218
  Planarity :  0.004   0.085   1397
  Dihedral  :  5.505  31.600   1083
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.67 %
    Favored  : 88.33 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 21.77 %
    Favored  : 73.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.31 (0.24), residues: 1003
  helix: -2.47 (0.61), residues: 61
  sheet: -1.72 (0.43), residues: 154
  loop : -2.49 (0.20), residues: 788

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 245 
 TYR   0.022   0.002   TYR B 198 
 PHE   0.018   0.002   PHE C 192 
 TRP   0.023   0.002   TRP A 242 
 HIS   0.003   0.001   HIS C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 7856)
  covalent geometry    : angle       0.63705 (10704)
  hydrogen bonds       : bond        0.03520 (  111)
  hydrogen bonds       : angle       5.63840 (  327)

*********************** 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
  218 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 177
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 ASP cc_start: 0.7473 (m-30) cc_final: 0.7213 (p0)
REVERT: A   56 LYS cc_start: 0.8519 (tttm) cc_final: 0.8274 (tppt)
REVERT: A   80 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8316 (m)
REVERT: A   97 MET cc_start: 0.8181 (mtp) cc_final: 0.7842 (mtt)
REVERT: A  124 ASN cc_start: 0.9003 (m110) cc_final: 0.8574 (m110)
REVERT: A  213 LEU cc_start: 0.9235 (pt) cc_final: 0.8559 (pp)
REVERT: A  258 PHE cc_start: 0.8374 (m-10) cc_final: 0.7503 (m-10)
REVERT: A  318 PHE cc_start: 0.8686 (t80) cc_final: 0.8125 (t80)
REVERT: A  329 TYR cc_start: 0.8533 (t80) cc_final: 0.8274 (t80)
REVERT: B  195 GLU cc_start: 0.8371 (tp30) cc_final: 0.8067 (tp30)
REVERT: B  262 GLU cc_start: 0.8105 (tp30) cc_final: 0.7808 (mm-30)
REVERT: B  329 TYR cc_start: 0.9018 (t80) cc_final: 0.8570 (t80)
REVERT: B  348 THR cc_start: 0.8592 (m) cc_final: 0.8364 (p)
REVERT: B  354 ASN cc_start: 0.8301 (t0) cc_final: 0.8026 (t0)
REVERT: C   53 ASP cc_start: 0.8937 (m-30) cc_final: 0.8140 (t0)
REVERT: C   83 GLU cc_start: 0.7264 (mm-30) cc_final: 0.6934 (mm-30)
REVERT: C   91 GLN cc_start: 0.7324 (tp-100) cc_final: 0.6939 (tp-100)
REVERT: C   92 ARG cc_start: 0.8050 (mmt-90) cc_final: 0.7525 (mmt-90)
REVERT: C  131 ILE cc_start: 0.9199 (mt) cc_final: 0.8967 (mm)
  outliers start: 41
  outliers final: 35
  residues processed: 196
  average time/residue: 0.0597
  time to fit residues: 17.7350
Evaluate side-chains
  206 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 170
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
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  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  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   73 ILE
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue   94 LEU
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 2 optimal weight:    9.9990
   chunk 98 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   chunk 46 optimal weight:    7.9990
   chunk 43 optimal weight:    6.9990
   chunk 6 optimal weight:    0.2980
   chunk 16 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 91 optimal weight:    6.9990
   chunk 59 optimal weight:    6.9990
   overall best weight:    2.8588

-------------------------------------------------------------------------------
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 = 0.3469 r_free = 0.3469 target = 0.122199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.104038 restraints weight = 14108.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.107766 restraints weight = 7099.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.110322 restraints weight = 4385.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.112145 restraints weight = 3063.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.113382 restraints weight = 2310.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7856  Z= 0.190
  Angle     :  0.653  10.449  10704  Z= 0.345
  Chirality :  0.045   0.230   1218
  Planarity :  0.004   0.086   1397
  Dihedral  :  5.572  26.310   1083
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.86 %
    Favored  : 88.14 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 22.51 %
    Favored  : 72.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.33 (0.24), residues: 1003
  helix: -2.44 (0.59), residues: 61
  sheet: -1.75 (0.43), residues: 154
  loop : -2.51 (0.20), residues: 788

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 245 
 TYR   0.022   0.002   TYR B 198 
 PHE   0.013   0.002   PHE B 318 
 TRP   0.026   0.002   TRP A 242 
 HIS   0.003   0.001   HIS C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 7856)
  covalent geometry    : angle       0.65346 (10704)
  hydrogen bonds       : bond        0.03595 (  111)
  hydrogen bonds       : angle       5.68591 (  327)

*********************** 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
  213 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 171
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 ASP cc_start: 0.7474 (m-30) cc_final: 0.7150 (p0)
REVERT: A   56 LYS cc_start: 0.8573 (tttm) cc_final: 0.8268 (tppt)
REVERT: A   80 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8300 (m)
REVERT: A   97 MET cc_start: 0.8249 (mtp) cc_final: 0.7922 (mtt)
REVERT: A  124 ASN cc_start: 0.9014 (m110) cc_final: 0.8603 (m110)
REVERT: A  213 LEU cc_start: 0.9224 (pt) cc_final: 0.8525 (pp)
REVERT: A  258 PHE cc_start: 0.8399 (m-10) cc_final: 0.7450 (m-10)
REVERT: A  318 PHE cc_start: 0.8700 (t80) cc_final: 0.8193 (t80)
REVERT: A  329 TYR cc_start: 0.8546 (t80) cc_final: 0.8310 (t80)
REVERT: B  195 GLU cc_start: 0.8372 (tp30) cc_final: 0.8068 (tp30)
REVERT: B  262 GLU cc_start: 0.8117 (tp30) cc_final: 0.7827 (mm-30)
REVERT: B  329 TYR cc_start: 0.9030 (t80) cc_final: 0.8580 (t80)
REVERT: B  348 THR cc_start: 0.8602 (m) cc_final: 0.8380 (p)
REVERT: B  354 ASN cc_start: 0.8309 (t0) cc_final: 0.8026 (t0)
REVERT: C   53 ASP cc_start: 0.8992 (m-30) cc_final: 0.8189 (t0)
REVERT: C   83 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7004 (mm-30)
REVERT: C   91 GLN cc_start: 0.7319 (tp-100) cc_final: 0.6936 (tp-100)
REVERT: C   92 ARG cc_start: 0.8031 (mmt-90) cc_final: 0.7508 (mmt-90)
REVERT: C  131 ILE cc_start: 0.9193 (mt) cc_final: 0.8963 (mm)
REVERT: C  299 GLN cc_start: 0.8358 (mt0) cc_final: 0.8135 (mt0)
  outliers start: 42
  outliers final: 36
  residues processed: 192
  average time/residue: 0.0566
  time to fit residues: 16.6566
Evaluate side-chains
  204 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 167
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
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  140 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  103 MET
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  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   94 LEU
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 90 optimal weight:    2.9990
   chunk 16 optimal weight:    8.9990
   chunk 24 optimal weight:    0.0060
   chunk 1 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 74 optimal weight:    6.9990
   chunk 69 optimal weight:    9.9990
   chunk 96 optimal weight:    3.9990
   chunk 3 optimal weight:    8.9990
   chunk 95 optimal weight:    3.9990
   overall best weight:    3.0004

-------------------------------------------------------------------------------
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 = 0.3460 r_free = 0.3460 target = 0.121455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.103425 restraints weight = 14114.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.107140 restraints weight = 7088.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.109651 restraints weight = 4397.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.111443 restraints weight = 3079.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.112748 restraints weight = 2327.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.2203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   7856  Z= 0.197
  Angle     :  0.662  10.772  10704  Z= 0.351
  Chirality :  0.046   0.231   1218
  Planarity :  0.004   0.085   1397
  Dihedral  :  5.629  24.402   1083
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.56 %
    Favored  : 87.44 %
  Rotamer:
    Outliers :  5.72 %
    Allowed  : 22.01 %
    Favored  : 72.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.27 (0.25), residues: 1003
  helix: -1.73 (0.72), residues: 49
  sheet: -1.78 (0.42), residues: 154
  loop : -2.51 (0.20), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 245 
 TYR   0.023   0.002   TYR B 198 
 PHE   0.013   0.002   PHE B 318 
 TRP   0.028   0.002   TRP A 242 
 HIS   0.003   0.001   HIS C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 7856)
  covalent geometry    : angle       0.66241 (10704)
  hydrogen bonds       : bond        0.03589 (  111)
  hydrogen bonds       : angle       5.71302 (  327)

*********************** 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
  221 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 175
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 ASP cc_start: 0.7569 (m-30) cc_final: 0.7191 (p0)
REVERT: A   56 LYS cc_start: 0.8574 (tttm) cc_final: 0.8285 (tppt)
REVERT: A   80 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8434 (m)
REVERT: A   97 MET cc_start: 0.8266 (mtp) cc_final: 0.7940 (mtt)
REVERT: A  124 ASN cc_start: 0.9029 (m110) cc_final: 0.8605 (m110)
REVERT: A  213 LEU cc_start: 0.9277 (pt) cc_final: 0.8566 (pp)
REVERT: A  228 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.8097 (p90)
REVERT: A  258 PHE cc_start: 0.8462 (m-10) cc_final: 0.7410 (m-10)
REVERT: A  318 PHE cc_start: 0.8761 (t80) cc_final: 0.8243 (t80)
REVERT: A  329 TYR cc_start: 0.8562 (t80) cc_final: 0.8341 (t80)
REVERT: B  195 GLU cc_start: 0.8326 (tp30) cc_final: 0.8024 (tp30)
REVERT: B  262 GLU cc_start: 0.8135 (tp30) cc_final: 0.7804 (mm-30)
REVERT: B  329 TYR cc_start: 0.9019 (t80) cc_final: 0.8616 (t80)
REVERT: B  335 ILE cc_start: 0.6939 (OUTLIER) cc_final: 0.6589 (tt)
REVERT: B  348 THR cc_start: 0.8662 (m) cc_final: 0.8444 (p)
REVERT: B  354 ASN cc_start: 0.8321 (t0) cc_final: 0.8041 (t0)
REVERT: C   53 ASP cc_start: 0.9072 (m-30) cc_final: 0.8230 (t0)
REVERT: C   83 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7015 (mm-30)
REVERT: C   91 GLN cc_start: 0.7353 (tp-100) cc_final: 0.6972 (tp-100)
REVERT: C   92 ARG cc_start: 0.8073 (mmt-90) cc_final: 0.7565 (mmt-90)
REVERT: C  131 ILE cc_start: 0.9195 (mt) cc_final: 0.8962 (mm)
REVERT: C  299 GLN cc_start: 0.8391 (mt0) cc_final: 0.8150 (mt0)
  outliers start: 46
  outliers final: 39
  residues processed: 200
  average time/residue: 0.0581
  time to fit residues: 17.5020
Evaluate side-chains
  208 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 166
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
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  140 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  228 PHE
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  103 MET
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  276 ILE
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  335 ILE
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   94 LEU
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  225 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 82 optimal weight:    9.9990
   chunk 90 optimal weight:    1.9990
   chunk 83 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 8 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9980
   chunk 5 optimal weight:    0.4980
   chunk 51 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 81 optimal weight:   20.0000
   chunk 86 optimal weight:    0.2980
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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 = 0.3508 r_free = 0.3508 target = 0.125269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.107159 restraints weight = 13968.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.110947 restraints weight = 7008.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.113536 restraints weight = 4329.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.115359 restraints weight = 3012.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.116657 restraints weight = 2270.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.2319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7856  Z= 0.123
  Angle     :  0.612   9.438  10704  Z= 0.324
  Chirality :  0.044   0.223   1218
  Planarity :  0.004   0.083   1397
  Dihedral  :  5.299  24.838   1083
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.97 %
    Favored  : 91.03 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 23.01 %
    Favored  : 72.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.19 (0.25), residues: 1003
  helix: -2.17 (0.62), residues: 61
  sheet: -1.64 (0.43), residues: 154
  loop : -2.43 (0.20), residues: 788

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 7856)
  covalent geometry    : angle       0.61242 (10704)
  hydrogen bonds       : bond        0.03164 (  111)
  hydrogen bonds       : angle       5.56961 (  327)

********************** 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
  221 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 183
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.8541 (tttm) cc_final: 0.8243 (tppt)
REVERT: A   80 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8291 (m)
REVERT: A   97 MET cc_start: 0.8202 (mtp) cc_final: 0.7863 (mtt)
REVERT: A  124 ASN cc_start: 0.8941 (m110) cc_final: 0.8503 (m110)
REVERT: A  213 LEU cc_start: 0.9108 (pt) cc_final: 0.8444 (pp)
REVERT: A  228 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.7908 (p90)
REVERT: A  258 PHE cc_start: 0.8377 (m-10) cc_final: 0.7452 (m-10)
REVERT: A  318 PHE cc_start: 0.8601 (t80) cc_final: 0.7992 (t80)
REVERT: A  329 TYR cc_start: 0.8557 (t80) cc_final: 0.8345 (t80)
REVERT: B  195 GLU cc_start: 0.8221 (tp30) cc_final: 0.7950 (tp30)
REVERT: B  262 GLU cc_start: 0.8140 (tp30) cc_final: 0.7887 (mm-30)
REVERT: B  329 TYR cc_start: 0.9081 (t80) cc_final: 0.8718 (t80)
REVERT: B  354 ASN cc_start: 0.8227 (t0) cc_final: 0.7948 (t0)
REVERT: C   53 ASP cc_start: 0.9038 (m-30) cc_final: 0.8225 (t0)
REVERT: C   83 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6968 (mm-30)
REVERT: C   91 GLN cc_start: 0.7284 (tp-100) cc_final: 0.6898 (tp-100)
REVERT: C   92 ARG cc_start: 0.7846 (mmt-90) cc_final: 0.7316 (mmt-90)
REVERT: C  177 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7783 (mm-30)
  outliers start: 38
  outliers final: 33
  residues processed: 200
  average time/residue: 0.0579
  time to fit residues: 17.4968
Evaluate side-chains
  211 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 176
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
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  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  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   94 LEU
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 2 optimal weight:    9.9990
   chunk 76 optimal weight:    7.9990
   chunk 35 optimal weight:    9.9990
   chunk 91 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0070
   chunk 50 optimal weight:    0.6980
   chunk 94 optimal weight:    0.8980
   chunk 25 optimal weight:    6.9990
   chunk 88 optimal weight:    7.9990
   chunk 87 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   overall best weight:    0.6800

-------------------------------------------------------------------------------
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 = 0.3534 r_free = 0.3534 target = 0.127539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.109552 restraints weight = 13971.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.113363 restraints weight = 6988.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.115962 restraints weight = 4291.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.117811 restraints weight = 2968.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.119109 restraints weight = 2224.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.2556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   7856  Z= 0.104
  Angle     :  0.590  10.268  10704  Z= 0.309
  Chirality :  0.044   0.260   1218
  Planarity :  0.003   0.045   1397
  Dihedral  :  5.142  51.082   1083
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 23.51 %
    Favored  : 72.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.99 (0.25), residues: 1003
  helix: -1.72 (0.72), residues: 55
  sheet: -1.35 (0.43), residues: 158
  loop : -2.35 (0.21), residues: 790

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 245 
 TYR   0.020   0.001   TYR B 198 
 PHE   0.008   0.001   PHE A 258 
 TRP   0.022   0.001   TRP A 242 
 HIS   0.001   0.000   HIS B 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 7856)
  covalent geometry    : angle       0.58980 (10704)
  hydrogen bonds       : bond        0.02980 (  111)
  hydrogen bonds       : angle       5.38915 (  327)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1432.67 seconds
wall clock time: 25 minutes 23.68 seconds (1523.68 seconds total)