Starting phenix.real_space_refine
on Wed Mar 12 12:17:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6kmf_0724/03_2025/6kmf_0724.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6kmf_0724/03_2025/6kmf_0724.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6kmf_0724/03_2025/6kmf_0724.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6kmf_0724/03_2025/6kmf_0724.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6kmf_0724/03_2025/6kmf_0724.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6kmf_0724/03_2025/6kmf_0724.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

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

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7704
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2403
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2403
          Classifications: {'peptide': 316}
          Link IDs: {'PTRANS': 13, 'TRANS': 302}
    Chain: "B"
      Number of atoms: 2568
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2568
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 323}
    Chain: "C"
      Number of atoms: 2568
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2568
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 323}
    Chain: "D"
      Number of atoms: 165
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 165
          Classifications: {'peptide': 21}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 20}
  Time building chain proxies: 5.63, per 1000 atoms: 0.73
  Number of scatterers: 7704
  At special positions: 0
  Unit cell: (170.24, 73.92, 181.44, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      27     16.00
     O    1524      8.00
     N    1293      7.00
     C    4860      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.85
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 20 sheets defined
      7.2% alpha, 26.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  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: 1.84

  Time building geometry restraints manager: 2.21 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:             2.710
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.500
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   7856  Z= 0.380
  Angle     :  0.901  10.181  10704  Z= 0.492
  Chirality :  0.058   0.290   1218
  Planarity :  0.006   0.067   1397
  Dihedral  : 14.663  83.107   2804
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.36 %
    Favored  : 86.64 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 14.80 %
    Favored  : 84.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.41 (0.21), residues: 1003
  helix: -4.98 (0.23), residues: 54
  sheet: -1.79 (0.44), residues: 144
  loop : -3.32 (0.17), residues: 805

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

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

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 221
  time to evaluate  : 0.803 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8511 (tttm) cc_final: 0.8212 (tppt)
REVERT: A   97 MET cc_start: 0.8361 (mtp) cc_final: 0.8097 (mtt)
REVERT: A  119 GLU cc_start: 0.8774 (mp0) cc_final: 0.8521 (mt-10)
REVERT: A  124 ASN cc_start: 0.9007 (m110) cc_final: 0.8525 (m110)
REVERT: A  182 MET cc_start: 0.8145 (mmt) cc_final: 0.7850 (mmt)
REVERT: A  200 LEU cc_start: 0.8614 (mt) cc_final: 0.8380 (mt)
REVERT: A  258 PHE cc_start: 0.8922 (m-80) cc_final: 0.8216 (m-80)
REVERT: A  259 TYR cc_start: 0.8845 (m-80) cc_final: 0.8619 (m-80)
REVERT: A  318 PHE cc_start: 0.8582 (t80) cc_final: 0.8088 (t80)
REVERT: B   92 ARG cc_start: 0.8386 (mmt-90) cc_final: 0.8122 (mmt-90)
REVERT: B  131 ILE cc_start: 0.8694 (mt) cc_final: 0.8492 (mp)
REVERT: B  195 GLU cc_start: 0.8091 (tp30) cc_final: 0.7828 (tp30)
REVERT: B  256 GLN cc_start: 0.8968 (mm110) cc_final: 0.8710 (mm-40)
REVERT: B  317 ASN cc_start: 0.8224 (t0) cc_final: 0.7981 (t0)
REVERT: B  329 TYR cc_start: 0.9064 (t80) cc_final: 0.8804 (t80)
REVERT: B  354 ASN cc_start: 0.8154 (t0) cc_final: 0.7870 (t0)
REVERT: C   53 ASP cc_start: 0.8274 (m-30) cc_final: 0.7866 (t0)
REVERT: C   83 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6971 (mm-30)
REVERT: C  236 ASN cc_start: 0.8181 (t0) cc_final: 0.7587 (t0)
  outliers start: 5
  outliers final: 2
  residues processed: 225
  average time/residue: 0.1756
  time to fit residues: 54.6472
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  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain B residue  316 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    0.6980
   chunk 75 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0470
   chunk 50 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 77 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   chunk 89 optimal weight:    4.9990
   overall best weight:    1.1484

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

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

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.124931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.107231 restraints weight = 13595.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.110907 restraints weight = 6934.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.113440 restraints weight = 4289.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.1472

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

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

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

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

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

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 205
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.6998 (p0)
REVERT: A   56 LYS cc_start: 0.8468 (tttm) cc_final: 0.8178 (tppt)
REVERT: A   80 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8128 (m)
REVERT: A   97 MET cc_start: 0.8234 (mtp) cc_final: 0.7928 (mtt)
REVERT: A  124 ASN cc_start: 0.9010 (m110) cc_final: 0.8601 (m110)
REVERT: A  182 MET cc_start: 0.8298 (mmt) cc_final: 0.7970 (mmt)
REVERT: A  213 LEU cc_start: 0.9111 (pt) cc_final: 0.8640 (pp)
REVERT: A  258 PHE cc_start: 0.8755 (m-80) cc_final: 0.8010 (m-80)
REVERT: A  318 PHE cc_start: 0.8493 (t80) cc_final: 0.7942 (t80)
REVERT: B  195 GLU cc_start: 0.8212 (tp30) cc_final: 0.7938 (tp30)
REVERT: B  256 GLN cc_start: 0.9002 (mm110) cc_final: 0.8701 (mm-40)
REVERT: B  317 ASN cc_start: 0.8177 (t0) cc_final: 0.7952 (t0)
REVERT: B  329 TYR cc_start: 0.9008 (t80) cc_final: 0.8593 (t80)
REVERT: B  348 THR cc_start: 0.8626 (m) cc_final: 0.8401 (p)
REVERT: B  354 ASN cc_start: 0.8165 (t0) cc_final: 0.7948 (t0)
REVERT: C   53 ASP cc_start: 0.8226 (m-30) cc_final: 0.7828 (t0)
REVERT: C   83 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6817 (mm-30)
REVERT: D  368 GLN cc_start: 0.7259 (tm-30) cc_final: 0.6797 (tm-30)
  outliers start: 30
  outliers final: 18
  residues processed: 221
  average time/residue: 0.1664
  time to fit residues: 54.3397
Evaluate side-chains
  202 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 182
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain C residue  278 CYS
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  330 THR
Chi-restraints excluded: chain C residue  335 ILE
Chi-restraints excluded: chain C residue  359 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 11 optimal weight:   30.0000
   chunk 53 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 76 optimal weight:    3.9990
   chunk 24 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.5988

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.124700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.107075 restraints weight = 14139.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.110786 restraints weight = 7125.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.113322 restraints weight = 4388.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.1728

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= 0.191
  Angle     :  0.596   9.317  10704  Z= 0.315
  Chirality :  0.044   0.257   1218
  Planarity :  0.004   0.074   1397
  Dihedral  :  5.566  47.992   1084
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.67 %
    Favored  : 90.33 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 19.15 %
    Favored  : 76.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.63 (0.24), residues: 1003
  helix: -3.67 (0.45), residues: 61
  sheet: -1.36 (0.45), residues: 144
  loop : -2.77 (0.19), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 242 
 HIS   0.002   0.001   HIS A 158 
 PHE   0.019   0.002   PHE C 192 
 TYR   0.021   0.002   TYR B 198 
 ARG   0.006   0.000   ARG B  92 

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

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 194
  time to evaluate  : 0.789 
Fit side-chains
REVERT: A   53 ASP cc_start: 0.7480 (m-30) cc_final: 0.7080 (p0)
REVERT: A   56 LYS cc_start: 0.8458 (tttm) cc_final: 0.8173 (tppt)
REVERT: A   80 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8154 (m)
REVERT: A   97 MET cc_start: 0.8228 (mtp) cc_final: 0.7935 (mtt)
REVERT: A  124 ASN cc_start: 0.9090 (m110) cc_final: 0.8647 (m110)
REVERT: A  182 MET cc_start: 0.8339 (mmt) cc_final: 0.8053 (mmt)
REVERT: A  213 LEU cc_start: 0.9206 (pt) cc_final: 0.8688 (pp)
REVERT: A  258 PHE cc_start: 0.8679 (m-80) cc_final: 0.7967 (m-80)
REVERT: A  318 PHE cc_start: 0.8555 (t80) cc_final: 0.7964 (t80)
REVERT: A  329 TYR cc_start: 0.8370 (t80) cc_final: 0.7945 (t80)
REVERT: B  195 GLU cc_start: 0.8106 (tp30) cc_final: 0.7823 (tp30)
REVERT: B  256 GLN cc_start: 0.8995 (mm110) cc_final: 0.8684 (mm-40)
REVERT: B  329 TYR cc_start: 0.9009 (t80) cc_final: 0.8572 (t80)
REVERT: B  348 THR cc_start: 0.8579 (m) cc_final: 0.8345 (p)
REVERT: B  354 ASN cc_start: 0.8189 (t0) cc_final: 0.7976 (t0)
REVERT: C   53 ASP cc_start: 0.8342 (m-30) cc_final: 0.7818 (t0)
REVERT: C   83 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6800 (mm-30)
REVERT: C  146 ASN cc_start: 0.7037 (OUTLIER) cc_final: 0.6827 (p0)
REVERT: D  368 GLN cc_start: 0.7336 (tm-30) cc_final: 0.6883 (tm-30)
  outliers start: 37
  outliers final: 26
  residues processed: 212
  average time/residue: 0.1408
  time to fit residues: 43.8287
Evaluate side-chains
  201 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 173
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  361 GLU
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   96 VAL
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 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  146 ASN
Chi-restraints excluded: chain C residue  148 ILE
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain C residue  278 CYS
Chi-restraints excluded: chain C residue  314 VAL
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  330 THR
Chi-restraints excluded: chain C residue  335 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    0.0870
   chunk 19 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 32 optimal weight:    0.5980
   chunk 71 optimal weight:    8.9990
   chunk 5 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 48 optimal weight:    9.9990
   chunk 63 optimal weight:    0.8980
   chunk 97 optimal weight:    9.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    1.3162

-------------------------------------------------------------------------------
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 = 0.3502 r_free = 0.3502 target = 0.125021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.107243 restraints weight = 13736.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.111055 restraints weight = 6758.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.113650 restraints weight = 4104.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.1898

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= 0.171
  Angle     :  0.582   9.440  10704  Z= 0.306
  Chirality :  0.044   0.254   1218
  Planarity :  0.004   0.073   1397
  Dihedral  :  5.418  44.919   1084
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 19.15 %
    Favored  : 76.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.44 (0.24), residues: 1003
  helix: -3.22 (0.52), residues: 61
  sheet: -1.31 (0.45), residues: 144
  loop : -2.64 (0.20), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 242 
 HIS   0.002   0.001   HIS A 158 
 PHE   0.021   0.001   PHE C 192 
 TYR   0.022   0.002   TYR B 198 
 ARG   0.005   0.000   ARG B  92 

*********************** 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
  228 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 189
  time to evaluate  : 0.885 
Fit side-chains
REVERT: A   53 ASP cc_start: 0.7388 (m-30) cc_final: 0.7085 (p0)
REVERT: A   56 LYS cc_start: 0.8449 (tttm) cc_final: 0.8156 (tppt)
REVERT: A   80 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8107 (m)
REVERT: A   97 MET cc_start: 0.8163 (mtp) cc_final: 0.7849 (mtt)
REVERT: A  124 ASN cc_start: 0.8908 (m110) cc_final: 0.8520 (m110)
REVERT: A  182 MET cc_start: 0.8355 (mmt) cc_final: 0.8085 (mmt)
REVERT: A  213 LEU cc_start: 0.9212 (pt) cc_final: 0.8596 (pp)
REVERT: A  318 PHE cc_start: 0.8586 (t80) cc_final: 0.7968 (t80)
REVERT: A  329 TYR cc_start: 0.8418 (t80) cc_final: 0.8022 (t80)
REVERT: B  195 GLU cc_start: 0.8119 (tp30) cc_final: 0.7838 (tp30)
REVERT: B  256 GLN cc_start: 0.9009 (mm110) cc_final: 0.8688 (mm-40)
REVERT: B  262 GLU cc_start: 0.8109 (tp30) cc_final: 0.7873 (mm-30)
REVERT: B  329 TYR cc_start: 0.9014 (t80) cc_final: 0.8572 (t80)
REVERT: B  348 THR cc_start: 0.8564 (m) cc_final: 0.8332 (p)
REVERT: B  354 ASN cc_start: 0.8177 (t0) cc_final: 0.7928 (t0)
REVERT: C   53 ASP cc_start: 0.8347 (m-30) cc_final: 0.7826 (t0)
REVERT: C   83 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6752 (mm-30)
REVERT: D  368 GLN cc_start: 0.7424 (tm-30) cc_final: 0.6921 (tm-30)
  outliers start: 39
  outliers final: 32
  residues processed: 205
  average time/residue: 0.1485
  time to fit residues: 44.2146
Evaluate side-chains
  217 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 184
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
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  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  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  360 THR
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  148 ILE
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain C residue  276 ILE
Chi-restraints excluded: chain C residue  278 CYS
Chi-restraints excluded: chain C residue  314 VAL
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  330 THR
Chi-restraints excluded: chain C residue  335 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 70 optimal weight:    8.9990
   chunk 42 optimal weight:    5.9990
   chunk 21 optimal weight:   10.0000
   chunk 89 optimal weight:    3.9990
   chunk 66 optimal weight:    8.9990
   chunk 77 optimal weight:    0.2980
   chunk 75 optimal weight:    3.9990
   chunk 98 optimal weight:    5.9990
   chunk 65 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    1.6184

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.124664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.106668 restraints weight = 13851.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.110451 restraints weight = 6865.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.113050 restraints weight = 4200.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.2042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7856  Z= 0.192
  Angle     :  0.593  10.319  10704  Z= 0.314
  Chirality :  0.044   0.278   1218
  Planarity :  0.004   0.077   1397
  Dihedral  :  5.341  40.390   1084
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.57 %
    Favored  : 90.43 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 19.65 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.33 (0.24), residues: 1003
  helix: -2.85 (0.56), residues: 61
  sheet: -1.59 (0.43), residues: 154
  loop : -2.51 (0.20), residues: 788

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 242 
 HIS   0.002   0.001   HIS C 170 
 PHE   0.020   0.001   PHE B  48 
 TYR   0.022   0.002   TYR C 280 
 ARG   0.003   0.000   ARG B  92 

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

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 191
  time to evaluate  : 0.787 
Fit side-chains
REVERT: A   53 ASP cc_start: 0.7484 (m-30) cc_final: 0.7192 (p0)
REVERT: A   56 LYS cc_start: 0.8478 (tttm) cc_final: 0.8187 (tppt)
REVERT: A   80 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8202 (m)
REVERT: A   97 MET cc_start: 0.8157 (mtp) cc_final: 0.7834 (mtt)
REVERT: A  124 ASN cc_start: 0.8902 (m110) cc_final: 0.8504 (m110)
REVERT: A  182 MET cc_start: 0.8292 (mmt) cc_final: 0.8023 (mmt)
REVERT: A  213 LEU cc_start: 0.9241 (pt) cc_final: 0.8576 (pp)
REVERT: A  318 PHE cc_start: 0.8623 (t80) cc_final: 0.8012 (t80)
REVERT: A  329 TYR cc_start: 0.8414 (t80) cc_final: 0.8065 (t80)
REVERT: A  336 GLU cc_start: 0.8250 (pt0) cc_final: 0.7948 (pt0)
REVERT: B   92 ARG cc_start: 0.8114 (mmt-90) cc_final: 0.7851 (mmt-90)
REVERT: B  195 GLU cc_start: 0.8181 (tp30) cc_final: 0.7848 (tp30)
REVERT: B  256 GLN cc_start: 0.9008 (mm110) cc_final: 0.8703 (mm-40)
REVERT: B  262 GLU cc_start: 0.8073 (tp30) cc_final: 0.7817 (mm-30)
REVERT: B  329 TYR cc_start: 0.9041 (t80) cc_final: 0.8554 (t80)
REVERT: B  348 THR cc_start: 0.8561 (m) cc_final: 0.8338 (p)
REVERT: B  354 ASN cc_start: 0.8262 (t0) cc_final: 0.7985 (t0)
REVERT: C   53 ASP cc_start: 0.8466 (m-30) cc_final: 0.7848 (t0)
REVERT: C   83 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6747 (mm-30)
REVERT: C   92 ARG cc_start: 0.7661 (mmt-90) cc_final: 0.7357 (mmt-90)
  outliers start: 43
  outliers final: 34
  residues processed: 212
  average time/residue: 0.1346
  time to fit residues: 41.9815
Evaluate side-chains
  215 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 180
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
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  182 MET
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  360 THR
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  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  278 CYS
Chi-restraints excluded: chain C residue  314 VAL
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  330 THR
Chi-restraints excluded: chain C residue  335 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 80 optimal weight:    7.9990
   chunk 4 optimal weight:    0.7980
   chunk 91 optimal weight:    3.9990
   chunk 60 optimal weight:    8.9990
   chunk 65 optimal weight:    6.9990
   chunk 26 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9990
   chunk 76 optimal weight:    7.9990
   chunk 36 optimal weight:    8.9990
   chunk 59 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    2.3588

-------------------------------------------------------------------------------
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 = 0.3477 r_free = 0.3477 target = 0.122897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.105196 restraints weight = 13683.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.108925 restraints weight = 6799.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.111453 restraints weight = 4161.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7856  Z= 0.246
  Angle     :  0.618  10.463  10704  Z= 0.327
  Chirality :  0.045   0.263   1218
  Planarity :  0.004   0.082   1397
  Dihedral  :  5.453  35.899   1084
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.87 %
    Favored  : 89.13 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 21.52 %
    Favored  : 73.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.27 (0.25), residues: 1003
  helix: -2.61 (0.59), residues: 61
  sheet: -1.64 (0.43), residues: 154
  loop : -2.46 (0.21), residues: 788

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 242 
 HIS   0.003   0.001   HIS C 170 
 PHE   0.022   0.002   PHE B  48 
 TYR   0.024   0.002   TYR B 198 
 ARG   0.002   0.000   ARG B  92 

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

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 181
  time to evaluate  : 0.963 
Fit side-chains
REVERT: A   53 ASP cc_start: 0.7444 (m-30) cc_final: 0.7141 (p0)
REVERT: A   56 LYS cc_start: 0.8499 (tttm) cc_final: 0.8240 (tppt)
REVERT: A   80 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8258 (m)
REVERT: A   97 MET cc_start: 0.8167 (mtp) cc_final: 0.7833 (mtt)
REVERT: A  124 ASN cc_start: 0.8979 (m110) cc_final: 0.8608 (m110)
REVERT: A  318 PHE cc_start: 0.8660 (t80) cc_final: 0.8096 (t80)
REVERT: A  329 TYR cc_start: 0.8480 (t80) cc_final: 0.8165 (t80)
REVERT: B  195 GLU cc_start: 0.8186 (tp30) cc_final: 0.7859 (tp30)
REVERT: B  262 GLU cc_start: 0.8089 (tp30) cc_final: 0.7801 (mm-30)
REVERT: B  329 TYR cc_start: 0.9059 (t80) cc_final: 0.8604 (t80)
REVERT: B  348 THR cc_start: 0.8595 (m) cc_final: 0.8374 (p)
REVERT: B  354 ASN cc_start: 0.8286 (t0) cc_final: 0.8022 (t0)
REVERT: C   83 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6879 (mm-30)
REVERT: C   91 GLN cc_start: 0.7254 (tp-100) cc_final: 0.6859 (tp-100)
REVERT: C   92 ARG cc_start: 0.7861 (mmt-90) cc_final: 0.7320 (mmt-90)
REVERT: C  131 ILE cc_start: 0.9207 (mt) cc_final: 0.8948 (mm)
REVERT: C  368 GLN cc_start: 0.7617 (tp-100) cc_final: 0.7279 (tp-100)
  outliers start: 38
  outliers final: 32
  residues processed: 197
  average time/residue: 0.1463
  time to fit residues: 42.8857
Evaluate side-chains
  204 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 171
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
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  214 VAL
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  161 ASN
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain C residue  276 ILE
Chi-restraints excluded: chain C residue  278 CYS
Chi-restraints excluded: chain C residue  314 VAL
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  330 THR
Chi-restraints excluded: chain C residue  335 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 34 optimal weight:   10.0000
   chunk 48 optimal weight:    0.2980
   chunk 18 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 75 optimal weight:    0.3980
   chunk 81 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 57 optimal weight:   10.0000
   chunk 36 optimal weight:    8.9990
   chunk 20 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    1.6984

-------------------------------------------------------------------------------
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 = 0.3491 r_free = 0.3491 target = 0.123967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.106049 restraints weight = 13925.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.109822 restraints weight = 6905.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.112381 restraints weight = 4223.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.2167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7856  Z= 0.200
  Angle     :  0.601   9.949  10704  Z= 0.318
  Chirality :  0.044   0.242   1218
  Planarity :  0.004   0.081   1397
  Dihedral  :  5.310  32.081   1084
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 22.76 %
    Favored  : 72.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.18 (0.25), residues: 1003
  helix: -2.34 (0.62), residues: 61
  sheet: -1.60 (0.43), residues: 154
  loop : -2.41 (0.21), residues: 788

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 242 
 HIS   0.002   0.001   HIS C 170 
 PHE   0.022   0.002   PHE B  48 
 TYR   0.022   0.001   TYR B 198 
 ARG   0.008   0.001   ARG B  92 

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

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 186
  time to evaluate  : 0.922 
Fit side-chains
REVERT: A   53 ASP cc_start: 0.7457 (m-30) cc_final: 0.7196 (p0)
REVERT: A   56 LYS cc_start: 0.8535 (tttm) cc_final: 0.8232 (tppt)
REVERT: A   80 THR cc_start: 0.8637 (OUTLIER) cc_final: 0.8258 (m)
REVERT: A   97 MET cc_start: 0.8148 (mtp) cc_final: 0.7814 (mtt)
REVERT: A  124 ASN cc_start: 0.8915 (m110) cc_final: 0.8504 (m110)
REVERT: A  213 LEU cc_start: 0.9164 (pt) cc_final: 0.8364 (pp)
REVERT: A  258 PHE cc_start: 0.8417 (m-10) cc_final: 0.7288 (m-10)
REVERT: A  318 PHE cc_start: 0.8634 (t80) cc_final: 0.8072 (t80)
REVERT: A  329 TYR cc_start: 0.8552 (t80) cc_final: 0.8291 (t80)
REVERT: A  336 GLU cc_start: 0.8271 (pt0) cc_final: 0.7976 (pt0)
REVERT: B  195 GLU cc_start: 0.8205 (tp30) cc_final: 0.7878 (tp30)
REVERT: B  262 GLU cc_start: 0.8137 (tp30) cc_final: 0.7862 (mm-30)
REVERT: B  329 TYR cc_start: 0.9084 (t80) cc_final: 0.8716 (t80)
REVERT: B  348 THR cc_start: 0.8556 (m) cc_final: 0.8341 (p)
REVERT: B  354 ASN cc_start: 0.8248 (t0) cc_final: 0.7966 (t0)
REVERT: C   53 ASP cc_start: 0.8858 (m-30) cc_final: 0.8030 (t0)
REVERT: C   83 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6855 (mm-30)
REVERT: C   91 GLN cc_start: 0.7248 (tp-100) cc_final: 0.6853 (tp-100)
REVERT: C   92 ARG cc_start: 0.7870 (mmt-90) cc_final: 0.7323 (mmt-90)
  outliers start: 36
  outliers final: 31
  residues processed: 202
  average time/residue: 0.1343
  time to fit residues: 40.2575
Evaluate side-chains
  213 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 181
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
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   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  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   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  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 55 optimal weight:    0.0060
   chunk 13 optimal weight:    3.9990
   chunk 6 optimal weight:    0.1980
   chunk 27 optimal weight:    0.8980
   chunk 14 optimal weight:    0.3980
   chunk 37 optimal weight:    0.5980
   chunk 85 optimal weight:    0.9980
   chunk 12 optimal weight:    8.9990
   chunk 23 optimal weight:    6.9990
   chunk 75 optimal weight:    9.9990
   chunk 31 optimal weight:   10.0000
   overall best weight:    0.4196

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

Flipped N/Q/H residues before XYZ refinement:
A 357 ASN
B 219 ASN
B 317 ASN
C 146 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.129095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.110935 restraints weight = 13944.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.114824 restraints weight = 6957.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.117444 restraints weight = 4252.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.2490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   7856  Z= 0.148
  Angle     :  0.586  10.357  10704  Z= 0.307
  Chirality :  0.044   0.268   1218
  Planarity :  0.004   0.078   1397
  Dihedral  :  4.854  31.201   1083
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 24.13 %
    Favored  : 72.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.02 (0.25), residues: 1003
  helix: -2.13 (0.65), residues: 61
  sheet: -1.46 (0.43), residues: 154
  loop : -2.31 (0.21), residues: 788

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 242 
 HIS   0.001   0.000   HIS B 339 
 PHE   0.024   0.001   PHE B  48 
 TYR   0.020   0.001   TYR B 198 
 ARG   0.004   0.000   ARG B  92 

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

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 193
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 ASP cc_start: 0.7456 (m-30) cc_final: 0.7227 (p0)
REVERT: A   56 LYS cc_start: 0.8475 (tttm) cc_final: 0.8153 (tppt)
REVERT: A   80 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.7984 (m)
REVERT: A   97 MET cc_start: 0.8043 (mtp) cc_final: 0.7691 (mtt)
REVERT: A  124 ASN cc_start: 0.8862 (m110) cc_final: 0.8573 (m110)
REVERT: A  135 GLU cc_start: 0.7916 (pm20) cc_final: 0.7690 (pt0)
REVERT: A  213 LEU cc_start: 0.8915 (pt) cc_final: 0.8349 (pp)
REVERT: A  329 TYR cc_start: 0.8486 (t80) cc_final: 0.8278 (t80)
REVERT: B  195 GLU cc_start: 0.8038 (tp30) cc_final: 0.7716 (tp30)
REVERT: B  262 GLU cc_start: 0.8133 (tp30) cc_final: 0.7868 (mm-30)
REVERT: B  329 TYR cc_start: 0.9097 (t80) cc_final: 0.8784 (t80)
REVERT: B  354 ASN cc_start: 0.8145 (t0) cc_final: 0.7884 (t0)
REVERT: C   53 ASP cc_start: 0.8836 (m-30) cc_final: 0.7932 (t0)
REVERT: C   83 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6712 (mm-30)
REVERT: C   92 ARG cc_start: 0.7484 (mmt-90) cc_final: 0.6785 (mmt-90)
REVERT: D  368 GLN cc_start: 0.7348 (tm-30) cc_final: 0.6909 (tm-30)
  outliers start: 28
  outliers final: 16
  residues processed: 209
  average time/residue: 0.1893
  time to fit residues: 58.1828
Evaluate side-chains
  196 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 179
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain B residue   96 VAL
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  377 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  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 73 optimal weight:    0.0040
   chunk 55 optimal weight:    2.9990
   chunk 25 optimal weight:    9.9990
   chunk 43 optimal weight:   10.0000
   chunk 53 optimal weight:    9.9990
   chunk 85 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 91 optimal weight:    0.8980
   chunk 8 optimal weight:    9.9990
   chunk 92 optimal weight:    6.9990
   chunk 65 optimal weight:    7.9990
   overall best weight:    2.1798

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

Flipped N/Q/H residues before XYZ refinement:
B 219 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.122800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.104619 restraints weight = 14300.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.108351 restraints weight = 7129.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.110919 restraints weight = 4392.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.2460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   7856  Z= 0.241
  Angle     :  0.625  10.457  10704  Z= 0.329
  Chirality :  0.044   0.265   1218
  Planarity :  0.004   0.082   1397
  Dihedral  :  5.216  45.206   1082
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.67 %
    Favored  : 90.33 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 24.13 %
    Favored  : 72.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.03 (0.25), residues: 1003
  helix: -2.01 (0.65), residues: 61
  sheet: -1.26 (0.44), residues: 144
  loop : -2.37 (0.20), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.061   0.002   TRP A 242 
 HIS   0.002   0.001   HIS A 158 
 PHE   0.012   0.002   PHE A 258 
 TYR   0.026   0.002   TYR B 237 
 ARG   0.005   0.001   ARG B  92 

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

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 183
  time to evaluate  : 1.066 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8445 (tttm) cc_final: 0.8082 (tppt)
REVERT: A   80 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8181 (m)
REVERT: A   97 MET cc_start: 0.8105 (mtp) cc_final: 0.7769 (mtt)
REVERT: A  103 MET cc_start: 0.8935 (ttm) cc_final: 0.8645 (ttm)
REVERT: A  124 ASN cc_start: 0.8978 (m110) cc_final: 0.8532 (m110)
REVERT: A  135 GLU cc_start: 0.8116 (pm20) cc_final: 0.7758 (pt0)
REVERT: A  213 LEU cc_start: 0.9202 (pt) cc_final: 0.8410 (pp)
REVERT: A  228 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7885 (p90)
REVERT: A  258 PHE cc_start: 0.8268 (m-10) cc_final: 0.7769 (m-10)
REVERT: A  329 TYR cc_start: 0.8572 (t80) cc_final: 0.8315 (t80)
REVERT: B  182 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7583 (mmt)
REVERT: B  195 GLU cc_start: 0.8159 (tp30) cc_final: 0.7796 (tp30)
REVERT: B  262 GLU cc_start: 0.8065 (tp30) cc_final: 0.7789 (mm-30)
REVERT: B  329 TYR cc_start: 0.9116 (t80) cc_final: 0.8753 (t80)
REVERT: B  354 ASN cc_start: 0.8228 (t0) cc_final: 0.7915 (t0)
REVERT: C   53 ASP cc_start: 0.8919 (m-30) cc_final: 0.7996 (t0)
REVERT: C   83 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6769 (mm-30)
REVERT: C   92 ARG cc_start: 0.7817 (mmt-90) cc_final: 0.7508 (mmt-90)
REVERT: C  131 ILE cc_start: 0.9156 (mt) cc_final: 0.8886 (mm)
  outliers start: 31
  outliers final: 23
  residues processed: 199
  average time/residue: 0.1734
  time to fit residues: 51.5176
Evaluate side-chains
  205 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 179
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
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  214 VAL
Chi-restraints excluded: chain A residue  228 PHE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  229 ASN
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  161 ASN
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain C residue  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 79 optimal weight:    5.9990
   chunk 37 optimal weight:    4.9990
   chunk 91 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9980
   chunk 1 optimal weight:    5.9990
   chunk 5 optimal weight:    0.8980
   chunk 27 optimal weight:    6.9990
   chunk 56 optimal weight:    6.9990
   chunk 70 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   chunk 25 optimal weight:    7.9990
   overall best weight:    1.7182

-------------------------------------------------------------------------------
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 = 0.3441 r_free = 0.3441 target = 0.122433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.104467 restraints weight = 14275.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.108199 restraints weight = 7062.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.110760 restraints weight = 4317.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.2529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7856  Z= 0.212
  Angle     :  0.627  10.244  10704  Z= 0.330
  Chirality :  0.044   0.265   1218
  Planarity :  0.004   0.086   1397
  Dihedral  :  5.242  42.551   1082
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.97 %
    Favored  : 91.03 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 25.12 %
    Favored  : 71.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (0.25), residues: 1003
  helix: -1.81 (0.70), residues: 55
  sheet: -1.54 (0.42), residues: 154
  loop : -2.30 (0.21), residues: 794

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.076   0.002   TRP A 242 
 HIS   0.002   0.001   HIS C 170 
 PHE   0.021   0.002   PHE C 192 
 TYR   0.023   0.002   TYR B 198 
 ARG   0.009   0.001   ARG B  92 

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

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 183
  time to evaluate  : 0.911 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8465 (tttm) cc_final: 0.8130 (tppt)
REVERT: A   80 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8170 (m)
REVERT: A   97 MET cc_start: 0.8054 (mtp) cc_final: 0.7706 (mtt)
REVERT: A  124 ASN cc_start: 0.8972 (m110) cc_final: 0.8518 (m110)
REVERT: A  135 GLU cc_start: 0.8027 (pm20) cc_final: 0.7707 (pt0)
REVERT: A  213 LEU cc_start: 0.9116 (pt) cc_final: 0.8393 (pp)
REVERT: A  228 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.7945 (p90)
REVERT: A  258 PHE cc_start: 0.8270 (m-10) cc_final: 0.7701 (m-10)
REVERT: A  329 TYR cc_start: 0.8575 (t80) cc_final: 0.8326 (t80)
REVERT: B  195 GLU cc_start: 0.8175 (tp30) cc_final: 0.7832 (tp30)
REVERT: B  262 GLU cc_start: 0.8063 (tp30) cc_final: 0.7807 (mm-30)
REVERT: B  329 TYR cc_start: 0.9117 (t80) cc_final: 0.8757 (t80)
REVERT: B  354 ASN cc_start: 0.8220 (t0) cc_final: 0.7923 (t0)
REVERT: C   53 ASP cc_start: 0.8939 (m-30) cc_final: 0.8137 (t0)
REVERT: C   83 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6758 (mm-30)
REVERT: C   91 GLN cc_start: 0.7161 (tp-100) cc_final: 0.6768 (tp-100)
REVERT: C   92 ARG cc_start: 0.7812 (mmt-90) cc_final: 0.7285 (mmt-90)
REVERT: C  131 ILE cc_start: 0.9128 (mt) cc_final: 0.8857 (mm)
REVERT: C  141 LEU cc_start: 0.8714 (tp) cc_final: 0.8509 (tp)
  outliers start: 27
  outliers final: 21
  residues processed: 197
  average time/residue: 0.1511
  time to fit residues: 43.7592
Evaluate side-chains
  203 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 180
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
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  214 VAL
Chi-restraints excluded: chain A residue  228 PHE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  161 ASN
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain C residue  276 ILE
Chi-restraints excluded: chain C residue  314 VAL
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  330 THR
Chi-restraints excluded: chain C residue  335 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 16 optimal weight:    8.9990
   chunk 31 optimal weight:   10.0000
   chunk 48 optimal weight:    7.9990
   chunk 77 optimal weight:    7.9990
   chunk 76 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 35 optimal weight:   10.0000
   chunk 32 optimal weight:    1.9990
   chunk 17 optimal weight:    6.9990
   chunk 38 optimal weight:    0.0870
   overall best weight:    2.2166

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.121047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.103190 restraints weight = 14266.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.106894 restraints weight = 7040.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.109276 restraints weight = 4305.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.2548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7856  Z= 0.247
  Angle     :  0.640  10.157  10704  Z= 0.337
  Chirality :  0.044   0.260   1218
  Planarity :  0.004   0.086   1397
  Dihedral  :  5.334  41.321   1082
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.57 %
    Favored  : 89.43 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 25.25 %
    Favored  : 71.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.02 (0.25), residues: 1003
  helix: -1.81 (0.69), residues: 55
  sheet: -1.57 (0.42), residues: 154
  loop : -2.32 (0.21), residues: 794

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.072   0.002   TRP A 242 
 HIS   0.002   0.001   HIS C 170 
 PHE   0.014   0.002   PHE C  48 
 TYR   0.023   0.002   TYR B 198 
 ARG   0.009   0.001   ARG B  92 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2804.84 seconds
wall clock time: 50 minutes 49.69 seconds (3049.69 seconds total)