Starting phenix.real_space_refine
on Wed Feb  4 07:42:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9men_48218/02_2026/9men_48218.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9men_48218/02_2026/9men_48218.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9men_48218/02_2026/9men_48218.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9men_48218/02_2026/9men_48218.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9men_48218/02_2026/9men_48218.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9men_48218/02_2026/9men_48218.cif"
  }
  resolution = 3.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.026
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      49      5.16       5
     C    6221      2.51       5
     N    1478      2.21       5
     O    1533      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9281
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2277
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2277
          Classifications: {'peptide': 281}
          Link IDs: {'PTRANS': 10, 'TRANS': 270}
    Chain: "B"
      Number of atoms: 2282
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2282
          Classifications: {'peptide': 281}
          Link IDs: {'PTRANS': 10, 'TRANS': 270}
    Chain: "C"
      Number of atoms: 2282
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2282
          Classifications: {'peptide': 281}
          Link IDs: {'PTRANS': 10, 'TRANS': 270}
    Chain: "D"
      Number of atoms: 2282
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2282
          Classifications: {'peptide': 281}
          Link IDs: {'PTRANS': 10, 'TRANS': 270}
    Chain: "E"
      Number of atoms: 158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 158
          Classifications: {'peptide': 20}
          Link IDs: {'PTRANS': 2, 'TRANS': 17}
  Time building chain proxies: 2.08, per 1000 atoms: 0.22
  Number of scatterers: 9281
  At special positions: 0
  Unit cell: (95.7, 93.525, 95.7, 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      49     16.00
     O    1533      8.00
     N    1478      7.00
     C    6221      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 109 " - pdb=" SG  CYS A 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 109 " - pdb=" SG  CYS B 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 109 " - pdb=" SG  CYS C 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 109 " - pdb=" SG  CYS D 186 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 252.3 milliseconds
  

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2196

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 4 sheets defined
      79.3% alpha, 1.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 64
    Processing helix  chain 'A' and resid 72 through 90
      removed outlier: 4.440A  pdb=" N   TYR A  76 " --> pdb=" O   MET A  72 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   THR A  90 " --> pdb=" O   LEU A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 100
      removed outlier: 3.889A  pdb=" N   TRP A  94 " --> pdb=" O   THR A  90 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   VAL A  99 " --> pdb=" O   ALA A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 139
      removed outlier: 3.889A  pdb=" N   VAL A 124 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 154
    Processing helix  chain 'A' and resid 154 through 167
      removed outlier: 4.185A  pdb=" N   VAL A 158 " --> pdb=" O   LYS A 154 " (cutoff:3.500A)
      removed outlier: 4.750A  pdb=" N   ILE A 162 " --> pdb=" O   VAL A 158 " (cutoff:3.500A)
      Proline residue:  A 163  - end of helix
    Processing helix  chain 'A' and resid 168 through 174
    Processing helix  chain 'A' and resid 192 through 208
      removed outlier: 3.980A  pdb=" N   VAL A 196 " --> pdb=" O   ASN A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 227
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 237 through 266
      removed outlier: 3.988A  pdb=" N   THR A 241 " --> pdb=" O   ALA A 237 " (cutoff:3.500A)
      Proline residue:  A 254  - end of helix
    Processing helix  chain 'A' and resid 273 through 292
      removed outlier: 3.626A  pdb=" N   GLU A 277 " --> pdb=" O   GLY A 273 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   HIS A 281 " --> pdb=" O   GLU A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 296
      removed outlier: 3.505A  pdb=" N   CYS A 296 " --> pdb=" O   PHE A 293 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 293 through 296'
    Processing helix  chain 'A' and resid 297 through 305
    Processing helix  chain 'B' and resid 35 through 64
      Proline residue:  B  42  - end of helix
    Processing helix  chain 'B' and resid 72 through 90
      removed outlier: 4.254A  pdb=" N   TYR B  76 " --> pdb=" O   MET B  72 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   THR B  90 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 100
      removed outlier: 3.654A  pdb=" N   TRP B  94 " --> pdb=" O   THR B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 139
      removed outlier: 4.397A  pdb=" N   VAL B 124 " --> pdb=" O   LEU B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 154
    Processing helix  chain 'B' and resid 154 through 167
      removed outlier: 4.370A  pdb=" N   VAL B 158 " --> pdb=" O   LYS B 154 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   ILE B 162 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      Proline residue:  B 163  - end of helix
    Processing helix  chain 'B' and resid 168 through 174
    Processing helix  chain 'B' and resid 192 through 209
      removed outlier: 3.797A  pdb=" N   VAL B 196 " --> pdb=" O   ASN B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 227
      removed outlier: 3.642A  pdb=" N   SER B 227 " --> pdb=" O   ILE B 223 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 266
      Proline residue:  B 254  - end of helix
    Processing helix  chain 'B' and resid 275 through 291
      removed outlier: 3.768A  pdb=" N   SER B 285 " --> pdb=" O   HIS B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 304
      removed outlier: 4.204A  pdb=" N   CYS B 296 " --> pdb=" O   PHE B 292 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ASN B 298 " --> pdb=" O   HIS B 294 " (cutoff:3.500A)
      Proline residue:  B 299  - end of helix
    Processing helix  chain 'C' and resid 34 through 64
      Proline residue:  C  42  - end of helix
    Processing helix  chain 'C' and resid 72 through 100
      removed outlier: 4.052A  pdb=" N   TYR C  76 " --> pdb=" O   MET C  72 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   THR C  90 " --> pdb=" O   LEU C  86 " (cutoff:3.500A)
      Proline residue:  C  92  - end of helix
    Processing helix  chain 'C' and resid 104 through 139
      removed outlier: 4.534A  pdb=" N   LEU C 108 " --> pdb=" O   PHE C 104 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   CYS C 109 " --> pdb=" O   GLY C 105 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   VAL C 124 " --> pdb=" O   LEU C 120 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 145 through 154
    Processing helix  chain 'C' and resid 155 through 167
      removed outlier: 4.841A  pdb=" N   ILE C 162 " --> pdb=" O   VAL C 158 " (cutoff:3.500A)
      Proline residue:  C 163  - end of helix
    Processing helix  chain 'C' and resid 168 through 174
    Processing helix  chain 'C' and resid 192 through 209
      removed outlier: 3.733A  pdb=" N   VAL C 196 " --> pdb=" O   ASN C 192 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 227
      removed outlier: 3.686A  pdb=" N   SER C 227 " --> pdb=" O   ILE C 223 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 232 through 236
      removed outlier: 4.407A  pdb=" N   ARG C 235 " --> pdb=" O   HIS C 232 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 237 through 266
      removed outlier: 4.174A  pdb=" N   THR C 241 " --> pdb=" O   ALA C 237 " (cutoff:3.500A)
      Proline residue:  C 254  - end of helix
      removed outlier: 3.676A  pdb=" N   LEU C 266 " --> pdb=" O   ASP C 262 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 267 through 269
      No H-bonds generated for 'chain 'C' and resid 267 through 269'
    Processing helix  chain 'C' and resid 274 through 292
      removed outlier: 3.603A  pdb=" N   SER C 285 " --> pdb=" O   HIS C 281 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 293 through 304
      removed outlier: 4.347A  pdb=" N   ASN C 298 " --> pdb=" O   HIS C 294 " (cutoff:3.500A)
      Proline residue:  C 299  - end of helix
    Processing helix  chain 'D' and resid 36 through 64
      Proline residue:  D  42  - end of helix
    Processing helix  chain 'D' and resid 71 through 100
      removed outlier: 3.984A  pdb=" N   LYS D  75 " --> pdb=" O   SER D  71 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   TYR D  76 " --> pdb=" O   MET D  72 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   THR D  90 " --> pdb=" O   LEU D  86 " (cutoff:3.500A)
      Proline residue:  D  92  - end of helix
    Processing helix  chain 'D' and resid 105 through 140
      removed outlier: 3.503A  pdb=" N   CYS D 109 " --> pdb=" O   GLY D 105 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   VAL D 124 " --> pdb=" O   LEU D 120 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 145 through 154
    Processing helix  chain 'D' and resid 155 through 167
      removed outlier: 4.805A  pdb=" N   ILE D 162 " --> pdb=" O   VAL D 158 " (cutoff:3.500A)
      Proline residue:  D 163  - end of helix
    Processing helix  chain 'D' and resid 168 through 174
    Processing helix  chain 'D' and resid 192 through 209
      removed outlier: 3.735A  pdb=" N   VAL D 196 " --> pdb=" O   ASN D 192 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 209 through 227
      removed outlier: 3.529A  pdb=" N   SER D 227 " --> pdb=" O   ILE D 223 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 232 through 234
      No H-bonds generated for 'chain 'D' and resid 232 through 234'
    Processing helix  chain 'D' and resid 235 through 266
      removed outlier: 3.692A  pdb=" N   LYS D 239 " --> pdb=" O   ARG D 235 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   THR D 240 " --> pdb=" O   LYS D 236 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   THR D 241 " --> pdb=" O   ALA D 237 " (cutoff:3.500A)
      Proline residue:  D 254  - end of helix
    Processing helix  chain 'D' and resid 273 through 292
      removed outlier: 3.566A  pdb=" N   GLU D 277 " --> pdb=" O   GLY D 273 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ASN D 278 " --> pdb=" O   CYS D 274 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   SER D 285 " --> pdb=" O   HIS D 281 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 293 through 304
      removed outlier: 3.986A  pdb=" N   ASN D 298 " --> pdb=" O   HIS D 294 " (cutoff:3.500A)
      Proline residue:  D 299  - end of helix
      removed outlier: 3.503A  pdb=" N   TYR D 302 " --> pdb=" O   ASN D 298 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 177
    Processing sheet with id=AA2, first strand: chain 'B' and resid 175 through 177
      removed outlier: 3.599A  pdb=" N   ASN B 176 " --> pdb=" O   ASP B 187 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ASP B 187 " --> pdb=" O   ASN B 176 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 175 through 177
      removed outlier: 3.637A  pdb=" N   ASN C 176 " --> pdb=" O   ASP C 187 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 175 through 177
      removed outlier: 3.834A  pdb=" N   ASN D 176 " --> pdb=" O   ASP D 187 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ASP D 187 " --> pdb=" O   ASN D 176 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    611 hydrogen bonds defined for protein.
    1830 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: 1.28

  Time building geometry restraints manager: 0.80 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2723
        1.35 -     1.47: 2516
        1.47 -     1.59: 4240
        1.59 -     1.71: 0
        1.71 -     1.83: 62
  Bond restraints: 9541
  Sorted by residual:
  bond pdb=" CB  ASN C 143 "
       pdb=" CG  ASN C 143 "
    ideal  model  delta    sigma   weight residual
    1.516  1.569 -0.053 2.50e-02 1.60e+03 4.54e+00
  bond pdb=" CB  ASP D 133 "
       pdb=" CG  ASP D 133 "
    ideal  model  delta    sigma   weight residual
    1.516  1.567 -0.051 2.50e-02 1.60e+03 4.15e+00
  bond pdb=" C   LEU D  41 "
       pdb=" N   PRO D  42 "
    ideal  model  delta    sigma   weight residual
    1.334  1.381 -0.047 2.34e-02 1.83e+03 3.99e+00
  bond pdb=" C   LEU A  91 "
       pdb=" N   PRO A  92 "
    ideal  model  delta    sigma   weight residual
    1.335  1.356 -0.021 1.19e-02 7.06e+03 3.22e+00
  bond pdb=" CB  GLU B  26 "
       pdb=" CG  GLU B  26 "
    ideal  model  delta    sigma   weight residual
    1.520  1.573 -0.053 3.00e-02 1.11e+03 3.13e+00
  ... (remaining 9536 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.47: 12860
        4.47 -     8.93: 116
        8.93 -    13.40: 13
       13.40 -    17.87: 1
       17.87 -    22.34: 1
  Bond angle restraints: 12991
  Sorted by residual:
  angle pdb=" CA  LEU B 267 "
        pdb=" CB  LEU B 267 "
        pdb=" CG  LEU B 267 "
      ideal   model   delta    sigma   weight residual
     116.30  138.64  -22.34 3.50e+00 8.16e-02 4.07e+01
  angle pdb=" CA  LEU B  41 "
        pdb=" CB  LEU B  41 "
        pdb=" CG  LEU B  41 "
      ideal   model   delta    sigma   weight residual
     116.30  133.03  -16.73 3.50e+00 8.16e-02 2.29e+01
  angle pdb=" C   GLU B  31 "
        pdb=" N   GLU B  32 "
        pdb=" CA  GLU B  32 "
      ideal   model   delta    sigma   weight residual
     121.54  130.13   -8.59 1.91e+00 2.74e-01 2.02e+01
  angle pdb=" N   VAL A 160 "
        pdb=" CA  VAL A 160 "
        pdb=" C   VAL A 160 "
      ideal   model   delta    sigma   weight residual
     111.62  108.12    3.50 7.90e-01 1.60e+00 1.96e+01
  angle pdb=" C   ALA B  34 "
        pdb=" N   ASN B  35 "
        pdb=" CA  ASN B  35 "
      ideal   model   delta    sigma   weight residual
     121.54  129.59   -8.05 1.91e+00 2.74e-01 1.78e+01
  ... (remaining 12986 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.50: 4565
       16.50 -    33.00: 736
       33.00 -    49.49: 208
       49.49 -    65.99: 35
       65.99 -    82.49: 9
  Dihedral angle restraints: 5553
    sinusoidal: 2162
      harmonic: 3391
  Sorted by residual:
  dihedral pdb=" CA  LEU B 266 "
           pdb=" C   LEU B 266 "
           pdb=" N   LEU B 267 "
           pdb=" CA  LEU B 267 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.30  -25.70     0      5.00e+00 4.00e-02 2.64e+01
  dihedral pdb=" CA  LEU E 303 "
           pdb=" C   LEU E 303 "
           pdb=" N   PRO E 304 "
           pdb=" CA  PRO E 304 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.35  -24.65     0      5.00e+00 4.00e-02 2.43e+01
  dihedral pdb=" CA  THR A  90 "
           pdb=" C   THR A  90 "
           pdb=" N   LEU A  91 "
           pdb=" CA  LEU A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.74   21.26     0      5.00e+00 4.00e-02 1.81e+01
  ... (remaining 5550 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 1319
       0.080 -    0.159: 180
       0.159 -    0.239: 13
       0.239 -    0.319: 4
       0.319 -    0.399: 4
  Chirality restraints: 1520
  Sorted by residual:
  chirality pdb=" CG  LEU B  41 "
            pdb=" CB  LEU B  41 "
            pdb=" CD1 LEU B  41 "
            pdb=" CD2 LEU B  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.19   -0.40 2.00e-01 2.50e+01 3.97e+00
  chirality pdb=" CG  LEU B 165 "
            pdb=" CB  LEU B 165 "
            pdb=" CD1 LEU B 165 "
            pdb=" CD2 LEU B 165 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.21   -0.38 2.00e-01 2.50e+01 3.66e+00
  chirality pdb=" CB  VAL C 155 "
            pdb=" CA  VAL C 155 "
            pdb=" CG1 VAL C 155 "
            pdb=" CG2 VAL C 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.26   -0.37 2.00e-01 2.50e+01 3.39e+00
  ... (remaining 1517 not shown)

  Planarity restraints: 1566
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  91 "    0.050 5.00e-02 4.00e+02   7.51e-02 9.01e+00
        pdb=" N   PRO A  92 "   -0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO A  92 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A  92 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 183 "   -0.013 2.00e-02 2.50e+03   2.53e-02 6.40e+00
        pdb=" C   ARG A 183 "    0.044 2.00e-02 2.50e+03
        pdb=" O   ARG A 183 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   TYR A 184 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE D  53 "   -0.012 2.00e-02 2.50e+03   2.33e-02 5.41e+00
        pdb=" C   ILE D  53 "    0.040 2.00e-02 2.50e+03
        pdb=" O   ILE D  53 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   VAL D  54 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1563 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2742
        2.82 -     3.34: 8561
        3.34 -     3.86: 15772
        3.86 -     4.38: 16665
        4.38 -     4.90: 29869
  Nonbonded interactions: 73609
  Sorted by model distance:
  nonbonded pdb=" O   THR D 168 "
            pdb=" OG1 THR D 168 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OE1 GLN A  66 "
            pdb=" OG  SER C 227 "
     model   vdw
     2.325 3.040
  nonbonded pdb=" OD1 ASP B  74 "
            pdb=" OH  TYR B 302 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" OD1 ASP A  74 "
            pdb=" OH  TYR A 302 "
     model   vdw
     2.331 3.040
  nonbonded pdb=" OG  SER A 227 "
            pdb=" OE1 GLN B  66 "
     model   vdw
     2.332 3.040
  ... (remaining 73604 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' and resid 26 through 305)
  selection = (chain 'B' and resid 26 through 305)
  selection = (chain 'C' and resid 26 through 305)
  selection = (chain 'D' and resid 26 through 305)
}

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:             5.950
  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:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     7.930
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
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      :  0.005   0.058   9545  Z= 0.244
  Angle     :  1.087  22.337  12999  Z= 0.548
  Chirality :  0.058   0.399   1520
  Planarity :  0.007   0.075   1566
  Dihedral  : 17.477  82.491   3345
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 30.04 %
    Favored  : 68.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.99 (0.22), residues: 1134
  helix: -0.75 (0.16), residues: 860
  sheet:  None (None), residues: 0
  loop : -2.81 (0.33), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 183 
 TYR   0.013   0.001   TYR A 103 
 PHE   0.012   0.001   PHE D 199 
 TRP   0.023   0.001   TRP A  94 
 HIS   0.006   0.001   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 ( 9541)
  covalent geometry    : angle       1.08616 (12991)
  SS BOND              : bond        0.00247 (    4)
  SS BOND              : angle       1.80362 (    8)
  hydrogen bonds       : bond        0.09810 (  611)
  hydrogen bonds       : angle       6.01619 ( 1830)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 300
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A   97 ASP cc_start: 0.7573 (t0) cc_final: 0.7328 (t0)
REVERT: A  113 HIS cc_start: 0.8310 (m-70) cc_final: 0.8027 (m-70)
REVERT: A  182 ASP cc_start: 0.6850 (p0) cc_final: 0.6614 (p0)
REVERT: A  267 LEU cc_start: 0.8408 (mm) cc_final: 0.7992 (mp)
REVERT: B   41 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8085 (mm)
REVERT: B  157 TYR cc_start: 0.8284 (m-80) cc_final: 0.8044 (m-80)
REVERT: B  184 TYR cc_start: 0.7095 (m-10) cc_final: 0.6608 (m-10)
REVERT: C  119 ASN cc_start: 0.8663 (t0) cc_final: 0.8422 (t0)
REVERT: C  145 GLN cc_start: 0.7284 (tm-30) cc_final: 0.6908 (tm-30)
REVERT: C  184 TYR cc_start: 0.6974 (m-80) cc_final: 0.6508 (m-80)
REVERT: D   70 ARG cc_start: 0.6057 (tpt170) cc_final: 0.4961 (ptm160)
REVERT: D  162 ILE cc_start: 0.8804 (mm) cc_final: 0.8589 (mm)
REVERT: D  166 LEU cc_start: 0.8384 (tt) cc_final: 0.8058 (mt)
REVERT: D  193 ASP cc_start: 0.8211 (m-30) cc_final: 0.7416 (t70)
REVERT: D  233 GLN cc_start: 0.5523 (tm-30) cc_final: 0.5228 (tt0)
REVERT: D  272 GLN cc_start: 0.4917 (pm20) cc_final: 0.3929 (pm20)
  outliers start: 12
  outliers final: 1
  residues processed: 308
  average time/residue: 0.0772
  time to fit residues: 33.4639
Evaluate side-chains
  191 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 189
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue   88 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9980
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    1.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 272 GLN
B 145 GLN
B 281 HIS
B 298 ASN
C  35 ASN
C 281 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.105383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.088643 restraints weight = 22476.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.090954 restraints weight = 11068.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.093272 restraints weight = 7334.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.095030 restraints weight = 5134.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.095864 restraints weight = 3984.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.2116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9545  Z= 0.145
  Angle     :  0.658  12.348  12999  Z= 0.328
  Chirality :  0.042   0.218   1520
  Planarity :  0.005   0.066   1566
  Dihedral  :  4.821  32.334   1234
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 28.47 %
    Favored  : 67.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.25), residues: 1134
  helix:  0.65 (0.18), residues: 860
  sheet:  None (None), residues: 0
  loop : -2.68 (0.34), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C 146 
 TYR   0.018   0.001   TYR D 116 
 PHE   0.019   0.001   PHE C  87 
 TRP   0.016   0.001   TRP C  94 
 HIS   0.004   0.001   HIS C 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 9541)
  covalent geometry    : angle       0.65796 (12991)
  SS BOND              : bond        0.00170 (    4)
  SS BOND              : angle       1.21283 (    8)
  hydrogen bonds       : bond        0.04136 (  611)
  hydrogen bonds       : angle       4.78413 ( 1830)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 213
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
REVERT: A   97 ASP cc_start: 0.7920 (t0) cc_final: 0.7689 (t0)
REVERT: A  287 THR cc_start: 0.9145 (m) cc_final: 0.8901 (p)
REVERT: A  300 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.9103 (mt)
REVERT: C  119 ASN cc_start: 0.8938 (t0) cc_final: 0.8669 (t0)
REVERT: C  145 GLN cc_start: 0.7354 (tm-30) cc_final: 0.6764 (tm-30)
REVERT: C  150 LEU cc_start: 0.8844 (mt) cc_final: 0.8594 (tp)
REVERT: C  184 TYR cc_start: 0.7131 (m-80) cc_final: 0.6547 (m-80)
REVERT: D   70 ARG cc_start: 0.6357 (tpt170) cc_final: 0.5013 (ptm160)
REVERT: D  162 ILE cc_start: 0.8846 (mm) cc_final: 0.8440 (mm)
REVERT: D  166 LEU cc_start: 0.8648 (tt) cc_final: 0.8147 (mt)
REVERT: D  172 PHE cc_start: 0.8842 (t80) cc_final: 0.8524 (t80)
REVERT: D  193 ASP cc_start: 0.8374 (m-30) cc_final: 0.7441 (t70)
REVERT: D  272 GLN cc_start: 0.5262 (pm20) cc_final: 0.4036 (pm20)
REVERT: D  277 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7629 (mp0)
  outliers start: 42
  outliers final: 20
  residues processed: 241
  average time/residue: 0.0743
  time to fit residues: 26.0714
Evaluate side-chains
  202 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 181
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  186 CYS
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  281 HIS
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  138 ILE
Chi-restraints excluded: chain C residue  168 THR
Chi-restraints excluded: chain C residue  186 CYS
Chi-restraints excluded: chain C residue  296 CYS
Chi-restraints excluded: chain C residue  297 LEU
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain D residue  165 LEU
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  274 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 90 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 95 optimal weight:    8.9990
   chunk 77 optimal weight:    0.5980
   chunk 109 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0970
   chunk 9 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 100 optimal weight:    1.9990
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 281 HIS
D 101 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.104847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.089060 restraints weight = 22504.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.091422 restraints weight = 11103.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.093629 restraints weight = 7288.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.094658 restraints weight = 5143.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.095508 restraints weight = 4223.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.2512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9545  Z= 0.125
  Angle     :  0.619  10.333  12999  Z= 0.308
  Chirality :  0.042   0.233   1520
  Planarity :  0.004   0.067   1566
  Dihedral  :  4.576  31.970   1233
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 27.69 %
    Favored  : 67.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.31 (0.26), residues: 1134
  helix:  1.10 (0.18), residues: 865
  sheet:  None (None), residues: 0
  loop : -2.77 (0.34), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  30 
 TYR   0.020   0.001   TYR D 116 
 PHE   0.022   0.001   PHE C  87 
 TRP   0.020   0.001   TRP C  94 
 HIS   0.003   0.001   HIS A 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 9541)
  covalent geometry    : angle       0.61872 (12991)
  SS BOND              : bond        0.00131 (    4)
  SS BOND              : angle       0.96361 (    8)
  hydrogen bonds       : bond        0.03917 (  611)
  hydrogen bonds       : angle       4.61265 ( 1830)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 206
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7275 (t0)
REVERT: A   97 ASP cc_start: 0.7899 (t0) cc_final: 0.7663 (t0)
REVERT: A  287 THR cc_start: 0.9157 (m) cc_final: 0.8925 (p)
REVERT: B  131 SER cc_start: 0.8902 (OUTLIER) cc_final: 0.8526 (t)
REVERT: C  102 TRP cc_start: 0.8031 (t-100) cc_final: 0.7743 (t-100)
REVERT: C  119 ASN cc_start: 0.8950 (t0) cc_final: 0.8678 (t0)
REVERT: C  153 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6766 (mm-30)
REVERT: C  172 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7112 (m-80)
REVERT: C  184 TYR cc_start: 0.7097 (m-80) cc_final: 0.6602 (m-80)
REVERT: D   70 ARG cc_start: 0.6282 (tpt170) cc_final: 0.4975 (ptm160)
REVERT: D   84 ASP cc_start: 0.8335 (m-30) cc_final: 0.8101 (m-30)
REVERT: D  162 ILE cc_start: 0.8869 (mm) cc_final: 0.8496 (mm)
REVERT: D  166 LEU cc_start: 0.8638 (tt) cc_final: 0.8138 (mt)
REVERT: D  193 ASP cc_start: 0.8341 (m-30) cc_final: 0.7458 (t70)
  outliers start: 45
  outliers final: 25
  residues processed: 241
  average time/residue: 0.0689
  time to fit residues: 24.6636
Evaluate side-chains
  209 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 181
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   84 ASP
Chi-restraints excluded: chain A residue  119 ASN
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  186 CYS
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  186 CYS
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  282 LYS
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  168 THR
Chi-restraints excluded: chain C residue  172 PHE
Chi-restraints excluded: chain C residue  186 CYS
Chi-restraints excluded: chain C residue  296 CYS
Chi-restraints excluded: chain C residue  297 LEU
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain D residue  186 CYS
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  274 CYS
Chi-restraints excluded: chain D residue  295 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 81 optimal weight:    4.9990
   chunk 76 optimal weight:   10.0000
   chunk 92 optimal weight:    0.7980
   chunk 105 optimal weight:   10.0000
   chunk 93 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 202 GLN
B 113 HIS
C 281 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.106228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.090058 restraints weight = 22498.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.092733 restraints weight = 11210.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.094765 restraints weight = 7274.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.096124 restraints weight = 5183.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.096587 restraints weight = 4160.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.2801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9545  Z= 0.129
  Angle     :  0.610   9.548  12999  Z= 0.305
  Chirality :  0.042   0.242   1520
  Planarity :  0.004   0.068   1566
  Dihedral  :  4.353  20.398   1231
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 27.98 %
    Favored  : 66.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.26), residues: 1134
  helix:  1.31 (0.18), residues: 865
  sheet:  None (None), residues: 0
  loop : -2.70 (0.34), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 146 
 TYR   0.012   0.001   TYR D 116 
 PHE   0.024   0.001   PHE C  87 
 TRP   0.022   0.001   TRP C  94 
 HIS   0.003   0.000   HIS A 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 9541)
  covalent geometry    : angle       0.60954 (12991)
  SS BOND              : bond        0.00109 (    4)
  SS BOND              : angle       0.95117 (    8)
  hydrogen bonds       : bond        0.03881 (  611)
  hydrogen bonds       : angle       4.55792 ( 1830)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 197
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7388 (t0)
REVERT: A   97 ASP cc_start: 0.7882 (t0) cc_final: 0.7678 (t0)
REVERT: A  287 THR cc_start: 0.9161 (m) cc_final: 0.8921 (p)
REVERT: B  113 HIS cc_start: 0.8331 (OUTLIER) cc_final: 0.8128 (m-70)
REVERT: B  131 SER cc_start: 0.8831 (OUTLIER) cc_final: 0.8440 (t)
REVERT: C  102 TRP cc_start: 0.8096 (t-100) cc_final: 0.7789 (t-100)
REVERT: C  153 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6793 (mm-30)
REVERT: C  172 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7147 (m-80)
REVERT: C  184 TYR cc_start: 0.7123 (m-80) cc_final: 0.6642 (m-80)
REVERT: D   38 LYS cc_start: 0.8971 (mttt) cc_final: 0.8541 (mtmt)
REVERT: D   70 ARG cc_start: 0.6249 (tpt170) cc_final: 0.5003 (ptm160)
REVERT: D  162 ILE cc_start: 0.8861 (mm) cc_final: 0.8459 (mm)
REVERT: D  166 LEU cc_start: 0.8590 (tt) cc_final: 0.8104 (mt)
REVERT: D  193 ASP cc_start: 0.8298 (m-30) cc_final: 0.7430 (t70)
REVERT: D  235 ARG cc_start: 0.7164 (ptp90) cc_final: 0.6852 (ptp90)
  outliers start: 54
  outliers final: 34
  residues processed: 231
  average time/residue: 0.0669
  time to fit residues: 22.9984
Evaluate side-chains
  220 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 182
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ASP
Chi-restraints excluded: chain A residue  119 ASN
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  186 CYS
Chi-restraints excluded: chain A residue  202 GLN
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain B residue  113 HIS
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  186 CYS
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  282 LYS
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  168 THR
Chi-restraints excluded: chain C residue  172 PHE
Chi-restraints excluded: chain C residue  186 CYS
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  205 MET
Chi-restraints excluded: chain C residue  297 LEU
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain D residue  165 LEU
Chi-restraints excluded: chain D residue  186 CYS
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  274 CYS
Chi-restraints excluded: chain D residue  295 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 97 optimal weight:    6.9990
   chunk 54 optimal weight:    5.9990
   chunk 76 optimal weight:    9.9990
   chunk 60 optimal weight:    8.9990
   chunk 52 optimal weight:    5.9990
   chunk 40 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 99 optimal weight:   10.0000
   chunk 46 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  35 ASN
** D 192 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 = 0.3479 r_free = 0.3479 target = 0.097815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.081136 restraints weight = 23092.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.083243 restraints weight = 11736.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.085415 restraints weight = 8030.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.086963 restraints weight = 5820.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.087497 restraints weight = 4589.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.3684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056   9545  Z= 0.321
  Angle     :  0.765   9.232  12999  Z= 0.399
  Chirality :  0.049   0.274   1520
  Planarity :  0.005   0.067   1566
  Dihedral  :  4.735  23.225   1231
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  7.83 %
    Allowed  : 24.85 %
    Favored  : 67.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.26), residues: 1134
  helix:  0.96 (0.18), residues: 860
  sheet:  None (None), residues: 0
  loop : -2.46 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  77 
 TYR   0.024   0.002   TYR C 219 
 PHE   0.028   0.002   PHE C  87 
 TRP   0.027   0.002   TRP C  94 
 HIS   0.034   0.002   HIS B 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00740 ( 9541)
  covalent geometry    : angle       0.76480 (12991)
  SS BOND              : bond        0.00305 (    4)
  SS BOND              : angle       1.45024 (    8)
  hydrogen bonds       : bond        0.05373 (  611)
  hydrogen bonds       : angle       5.03979 ( 1830)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 168
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 ASP cc_start: 0.9060 (OUTLIER) cc_final: 0.8782 (t0)
REVERT: B   70 ARG cc_start: 0.5806 (ptt180) cc_final: 0.5581 (ptp-170)
REVERT: B   91 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8945 (tt)
REVERT: B  136 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9338 (mm)
REVERT: B  169 ILE cc_start: 0.8814 (mm) cc_final: 0.8566 (mt)
REVERT: B  202 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8393 (tm-30)
REVERT: B  233 GLN cc_start: 0.5470 (pm20) cc_final: 0.5244 (pm20)
REVERT: C   69 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7489 (pp)
REVERT: C  153 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7006 (mm-30)
REVERT: C  172 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7672 (m-80)
REVERT: C  246 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8416 (mp)
REVERT: C  272 GLN cc_start: 0.7771 (mp10) cc_final: 0.7498 (mm-40)
REVERT: D   38 LYS cc_start: 0.8955 (mttt) cc_final: 0.8622 (mtmt)
REVERT: D   70 ARG cc_start: 0.6397 (tpt170) cc_final: 0.4992 (ptm160)
REVERT: D   84 ASP cc_start: 0.8138 (m-30) cc_final: 0.7866 (t0)
REVERT: D  165 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8708 (tt)
REVERT: D  166 LEU cc_start: 0.8830 (tt) cc_final: 0.8271 (mt)
REVERT: D  172 PHE cc_start: 0.8741 (t80) cc_final: 0.8485 (t80)
REVERT: D  193 ASP cc_start: 0.8294 (m-30) cc_final: 0.7460 (t70)
REVERT: D  235 ARG cc_start: 0.7177 (ptp90) cc_final: 0.6842 (ptp90)
  outliers start: 80
  outliers final: 42
  residues processed: 228
  average time/residue: 0.0704
  time to fit residues: 23.6846
Evaluate side-chains
  207 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 157
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  119 ASN
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  133 ASP
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  186 CYS
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain B residue  186 CYS
Chi-restraints excluded: chain B residue  202 GLN
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  281 HIS
Chi-restraints excluded: chain B residue  282 LYS
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  168 THR
Chi-restraints excluded: chain C residue  172 PHE
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  205 MET
Chi-restraints excluded: chain C residue  246 LEU
Chi-restraints excluded: chain C residue  262 ASP
Chi-restraints excluded: chain C residue  265 ILE
Chi-restraints excluded: chain C residue  297 LEU
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain D residue  165 LEU
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  240 THR
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  274 CYS
Chi-restraints excluded: chain D residue  284 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 56 optimal weight:    0.0010
   chunk 100 optimal weight:    9.9990
   chunk 36 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 84 optimal weight:    7.9990
   chunk 99 optimal weight:   10.0000
   chunk 11 optimal weight:    3.9990
   chunk 68 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9990
   chunk 94 optimal weight:    0.7980
   overall best weight:    0.6588

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

Flipped N/Q/H residues before XYZ refinement:
B 200 GLN
C 113 HIS
** C 278 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 = 0.3538 r_free = 0.3538 target = 0.102430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.085663 restraints weight = 22411.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.088258 restraints weight = 11208.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.090340 restraints weight = 7320.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.091720 restraints weight = 5311.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.092674 restraints weight = 4312.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.3542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9545  Z= 0.137
  Angle     :  0.636  10.498  12999  Z= 0.320
  Chirality :  0.043   0.262   1520
  Planarity :  0.004   0.067   1566
  Dihedral  :  4.536  20.437   1231
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 28.86 %
    Favored  : 66.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.26), residues: 1134
  helix:  1.34 (0.18), residues: 862
  sheet:  None (None), residues: 0
  loop : -2.28 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 146 
 TYR   0.015   0.001   TYR D 116 
 PHE   0.020   0.001   PHE C  87 
 TRP   0.028   0.001   TRP C  94 
 HIS   0.004   0.001   HIS B 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 9541)
  covalent geometry    : angle       0.63558 (12991)
  SS BOND              : bond        0.00117 (    4)
  SS BOND              : angle       1.36336 (    8)
  hydrogen bonds       : bond        0.04244 (  611)
  hydrogen bonds       : angle       4.67331 ( 1830)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 185
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 MET cc_start: 0.8529 (mmm) cc_final: 0.8317 (mmm)
REVERT: A   84 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7778 (t0)
REVERT: B   91 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8867 (tt)
REVERT: B  202 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8380 (tm-30)
REVERT: C  153 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6876 (mm-30)
REVERT: C  272 GLN cc_start: 0.7792 (mp10) cc_final: 0.7531 (mm-40)
REVERT: D   38 LYS cc_start: 0.8920 (mttt) cc_final: 0.8630 (mtmt)
REVERT: D   70 ARG cc_start: 0.6366 (tpt170) cc_final: 0.4998 (ptm160)
REVERT: D   84 ASP cc_start: 0.8073 (m-30) cc_final: 0.7772 (t0)
REVERT: D  153 GLU cc_start: 0.7454 (tp30) cc_final: 0.7070 (tp30)
REVERT: D  162 ILE cc_start: 0.8890 (mm) cc_final: 0.8512 (mm)
REVERT: D  166 LEU cc_start: 0.8722 (tt) cc_final: 0.8169 (mt)
REVERT: D  235 ARG cc_start: 0.7125 (ptp90) cc_final: 0.6627 (ttp-110)
  outliers start: 45
  outliers final: 30
  residues processed: 220
  average time/residue: 0.0816
  time to fit residues: 26.7097
Evaluate side-chains
  204 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 171
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   84 ASP
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  119 ASN
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  186 CYS
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  186 CYS
Chi-restraints excluded: chain B residue  202 GLN
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  281 HIS
Chi-restraints excluded: chain B residue  282 LYS
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain D residue  186 CYS
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  274 CYS
Chi-restraints excluded: chain E residue  305 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 98 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9990
   chunk 86 optimal weight:    0.5980
   chunk 96 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B 200 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.102983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.086108 restraints weight = 22346.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.088652 restraints weight = 11230.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.090590 restraints weight = 7430.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.091997 restraints weight = 5423.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.093186 restraints weight = 4427.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.3638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9545  Z= 0.140
  Angle     :  0.634   9.490  12999  Z= 0.319
  Chirality :  0.042   0.275   1520
  Planarity :  0.004   0.067   1566
  Dihedral  :  4.402  20.183   1231
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 29.35 %
    Favored  : 66.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.26), residues: 1134
  helix:  1.41 (0.18), residues: 865
  sheet:  None (None), residues: 0
  loop : -2.42 (0.37), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 146 
 TYR   0.015   0.001   TYR D 116 
 PHE   0.033   0.001   PHE C  87 
 TRP   0.028   0.001   TRP C  94 
 HIS   0.003   0.001   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 9541)
  covalent geometry    : angle       0.63342 (12991)
  SS BOND              : bond        0.00173 (    4)
  SS BOND              : angle       1.20012 (    8)
  hydrogen bonds       : bond        0.04141 (  611)
  hydrogen bonds       : angle       4.59335 ( 1830)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 177
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7863 (t0)
REVERT: B   91 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8880 (tt)
REVERT: B  127 LEU cc_start: 0.8720 (mt) cc_final: 0.8486 (mt)
REVERT: B  131 SER cc_start: 0.8857 (OUTLIER) cc_final: 0.8468 (t)
REVERT: B  202 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8363 (tm-30)
REVERT: C   63 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7381 (mtp)
REVERT: C  153 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6857 (mm-30)
REVERT: C  187 ASP cc_start: 0.8029 (t0) cc_final: 0.7798 (m-30)
REVERT: C  272 GLN cc_start: 0.7871 (mp10) cc_final: 0.7659 (mm-40)
REVERT: D   38 LYS cc_start: 0.8928 (mttt) cc_final: 0.8659 (mtmt)
REVERT: D   70 ARG cc_start: 0.6359 (tpt170) cc_final: 0.4971 (ptm160)
REVERT: D  153 GLU cc_start: 0.7431 (tp30) cc_final: 0.7049 (tp30)
REVERT: D  162 ILE cc_start: 0.8902 (mm) cc_final: 0.8521 (mm)
REVERT: D  166 LEU cc_start: 0.8733 (tt) cc_final: 0.8174 (mt)
REVERT: D  235 ARG cc_start: 0.7119 (ptp90) cc_final: 0.6810 (ptp90)
  outliers start: 41
  outliers final: 29
  residues processed: 209
  average time/residue: 0.0749
  time to fit residues: 23.4965
Evaluate side-chains
  204 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 170
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   84 ASP
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  119 ASN
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  186 CYS
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  274 CYS
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  186 CYS
Chi-restraints excluded: chain B residue  202 GLN
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  281 HIS
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue   63 MET
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  261 ILE
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain D residue  186 CYS
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  274 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 64 optimal weight:    0.0670
   chunk 15 optimal weight:   10.0000
   chunk 14 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 69 optimal weight:    0.5980
   chunk 111 optimal weight:    2.9990
   chunk 100 optimal weight:    5.9990
   chunk 84 optimal weight:    0.2980
   chunk 60 optimal weight:   10.0000
   chunk 3 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.5922

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

Flipped N/Q/H residues before XYZ refinement:
** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.103733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.087018 restraints weight = 22151.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.089573 restraints weight = 11058.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.091693 restraints weight = 7277.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.093146 restraints weight = 5311.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.093769 restraints weight = 4241.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.3643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9545  Z= 0.129
  Angle     :  0.631   9.489  12999  Z= 0.314
  Chirality :  0.042   0.277   1520
  Planarity :  0.004   0.068   1566
  Dihedral  :  4.341  19.253   1231
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 29.55 %
    Favored  : 66.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.94 (0.26), residues: 1134
  helix:  1.51 (0.18), residues: 865
  sheet:  None (None), residues: 0
  loop : -2.40 (0.37), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 146 
 TYR   0.010   0.001   TYR D 116 
 PHE   0.037   0.001   PHE C  87 
 TRP   0.029   0.001   TRP C  94 
 HIS   0.004   0.000   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 9541)
  covalent geometry    : angle       0.63127 (12991)
  SS BOND              : bond        0.00069 (    4)
  SS BOND              : angle       0.91067 (    8)
  hydrogen bonds       : bond        0.03972 (  611)
  hydrogen bonds       : angle       4.53150 ( 1830)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 181
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   91 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8861 (tt)
REVERT: B  131 SER cc_start: 0.8794 (OUTLIER) cc_final: 0.8416 (t)
REVERT: C   63 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.7184 (mtp)
REVERT: C  153 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6873 (mm-30)
REVERT: C  187 ASP cc_start: 0.8010 (t0) cc_final: 0.7803 (m-30)
REVERT: C  272 GLN cc_start: 0.7899 (mp10) cc_final: 0.7678 (mm-40)
REVERT: D   38 LYS cc_start: 0.8918 (mttt) cc_final: 0.8659 (mtmt)
REVERT: D   70 ARG cc_start: 0.6303 (tpt170) cc_final: 0.4984 (ptm160)
REVERT: D  153 GLU cc_start: 0.7408 (tp30) cc_final: 0.7051 (tp30)
REVERT: D  162 ILE cc_start: 0.8878 (mm) cc_final: 0.8405 (mm)
REVERT: D  166 LEU cc_start: 0.8679 (tt) cc_final: 0.8139 (mt)
REVERT: D  235 ARG cc_start: 0.7152 (ptp90) cc_final: 0.6822 (ptp90)
  outliers start: 42
  outliers final: 32
  residues processed: 212
  average time/residue: 0.0781
  time to fit residues: 24.8898
Evaluate side-chains
  208 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 173
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  119 ASN
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  186 CYS
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  186 CYS
Chi-restraints excluded: chain B residue  200 GLN
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  281 HIS
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue   63 MET
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  186 CYS
Chi-restraints excluded: chain C residue  261 ILE
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain D residue  186 CYS
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  274 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 69 optimal weight:    0.0970
   chunk 36 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 111 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 53 optimal weight:    0.4980
   chunk 13 optimal weight:    3.9990
   chunk 74 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.104279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.087522 restraints weight = 22068.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.090082 restraints weight = 11042.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.091941 restraints weight = 7268.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.093418 restraints weight = 5419.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.094317 restraints weight = 4362.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.3718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9545  Z= 0.130
  Angle     :  0.641   9.328  12999  Z= 0.317
  Chirality :  0.042   0.259   1520
  Planarity :  0.004   0.068   1566
  Dihedral  :  4.284  18.846   1231
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 30.23 %
    Favored  : 65.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.03 (0.26), residues: 1134
  helix:  1.59 (0.18), residues: 862
  sheet:  None (None), residues: 0
  loop : -2.34 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 183 
 TYR   0.007   0.001   TYR D 116 
 PHE   0.040   0.001   PHE C  87 
 TRP   0.031   0.001   TRP C  94 
 HIS   0.003   0.000   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9541)
  covalent geometry    : angle       0.64090 (12991)
  SS BOND              : bond        0.00060 (    4)
  SS BOND              : angle       0.88359 (    8)
  hydrogen bonds       : bond        0.03921 (  611)
  hydrogen bonds       : angle       4.47304 ( 1830)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 188
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7830 (t0)
REVERT: A  288 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8062 (mt-10)
REVERT: B   91 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8877 (tt)
REVERT: B  131 SER cc_start: 0.8698 (OUTLIER) cc_final: 0.8314 (t)
REVERT: B  202 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8345 (tm-30)
REVERT: C   63 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.7162 (mtp)
REVERT: C  153 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6814 (mm-30)
REVERT: C  272 GLN cc_start: 0.7929 (mp10) cc_final: 0.7692 (mm-40)
REVERT: D   38 LYS cc_start: 0.8929 (mttt) cc_final: 0.8667 (mtmt)
REVERT: D   70 ARG cc_start: 0.6294 (tpt170) cc_final: 0.4934 (ptm160)
REVERT: D  153 GLU cc_start: 0.7396 (tp30) cc_final: 0.7047 (tp30)
REVERT: D  162 ILE cc_start: 0.8877 (mm) cc_final: 0.8467 (mm)
REVERT: D  166 LEU cc_start: 0.8650 (tt) cc_final: 0.8128 (mt)
REVERT: D  233 GLN cc_start: 0.5856 (tm-30) cc_final: 0.5545 (tt0)
REVERT: D  235 ARG cc_start: 0.7116 (ptp90) cc_final: 0.6816 (ptp90)
  outliers start: 39
  outliers final: 29
  residues processed: 216
  average time/residue: 0.0771
  time to fit residues: 25.2278
Evaluate side-chains
  214 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 180
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   84 ASP
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  119 ASN
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  186 CYS
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  186 CYS
Chi-restraints excluded: chain B residue  202 GLN
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  281 HIS
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue   63 MET
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain D residue  186 CYS
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  274 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 92 optimal weight:    0.9980
   chunk 109 optimal weight:    0.8980
   chunk 72 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 104 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 87 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   chunk 49 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.103867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.087237 restraints weight = 22319.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.089830 restraints weight = 11086.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.091645 restraints weight = 7259.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.093278 restraints weight = 5417.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.094155 restraints weight = 4315.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.3803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9545  Z= 0.139
  Angle     :  0.651   9.238  12999  Z= 0.321
  Chirality :  0.042   0.242   1520
  Planarity :  0.004   0.068   1566
  Dihedral  :  4.269  18.894   1231
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 30.14 %
    Favored  : 65.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.26), residues: 1134
  helix:  1.60 (0.18), residues: 864
  sheet:  None (None), residues: 0
  loop : -2.36 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 183 
 TYR   0.009   0.001   TYR C 256 
 PHE   0.035   0.001   PHE C  87 
 TRP   0.032   0.001   TRP C  94 
 HIS   0.003   0.001   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 9541)
  covalent geometry    : angle       0.65058 (12991)
  SS BOND              : bond        0.00105 (    4)
  SS BOND              : angle       0.94450 (    8)
  hydrogen bonds       : bond        0.03984 (  611)
  hydrogen bonds       : angle       4.46091 ( 1830)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 182
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7924 (t0)
REVERT: A  288 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8102 (mt-10)
REVERT: B   91 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8895 (tt)
REVERT: B  202 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8341 (tm-30)
REVERT: C   63 MET cc_start: 0.7340 (mtp) cc_final: 0.7139 (mtp)
REVERT: C  153 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6820 (mm-30)
REVERT: C  184 TYR cc_start: 0.7387 (m-80) cc_final: 0.7036 (m-80)
REVERT: C  272 GLN cc_start: 0.7948 (mp10) cc_final: 0.7721 (mm-40)
REVERT: D   38 LYS cc_start: 0.8943 (mttt) cc_final: 0.8670 (mtmt)
REVERT: D   70 ARG cc_start: 0.6255 (tpt170) cc_final: 0.4963 (ptm160)
REVERT: D   84 ASP cc_start: 0.8185 (m-30) cc_final: 0.7835 (t0)
REVERT: D  153 GLU cc_start: 0.7419 (tp30) cc_final: 0.7068 (tp30)
REVERT: D  162 ILE cc_start: 0.8883 (mm) cc_final: 0.8475 (mm)
REVERT: D  166 LEU cc_start: 0.8659 (tt) cc_final: 0.8140 (mt)
REVERT: D  233 GLN cc_start: 0.5849 (tm-30) cc_final: 0.5536 (tt0)
REVERT: D  235 ARG cc_start: 0.7117 (ptp90) cc_final: 0.6811 (ptp90)
REVERT: D  274 CYS cc_start: 0.7280 (OUTLIER) cc_final: 0.7065 (m)
  outliers start: 41
  outliers final: 32
  residues processed: 210
  average time/residue: 0.0734
  time to fit residues: 23.3023
Evaluate side-chains
  214 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 178
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   84 ASP
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  119 ASN
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  186 CYS
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  186 CYS
Chi-restraints excluded: chain B residue  202 GLN
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  281 HIS
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  186 CYS
Chi-restraints excluded: chain C residue  261 ILE
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain D residue  165 LEU
Chi-restraints excluded: chain D residue  186 CYS
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  274 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 110 optimal weight:    0.6980
   chunk 82 optimal weight:    2.9990
   chunk 85 optimal weight:    0.4980
   chunk 79 optimal weight:    0.9980
   chunk 64 optimal weight:    0.0070
   chunk 43 optimal weight:    0.0060
   chunk 72 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   overall best weight:    0.4414

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

Flipped N/Q/H residues before XYZ refinement:
** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.105787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.089196 restraints weight = 21803.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.091812 restraints weight = 10950.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.093666 restraints weight = 7172.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.095438 restraints weight = 5339.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.096102 restraints weight = 4301.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.3869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9545  Z= 0.126
  Angle     :  0.648   9.523  12999  Z= 0.316
  Chirality :  0.042   0.224   1520
  Planarity :  0.004   0.069   1566
  Dihedral  :  4.206  17.794   1231
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 30.72 %
    Favored  : 65.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.14 (0.27), residues: 1134
  helix:  1.67 (0.18), residues: 864
  sheet:  None (None), residues: 0
  loop : -2.36 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 183 
 TYR   0.012   0.001   TYR A 256 
 PHE   0.036   0.001   PHE C  87 
 TRP   0.023   0.001   TRP C  94 
 HIS   0.003   0.000   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 9541)
  covalent geometry    : angle       0.64827 (12991)
  SS BOND              : bond        0.00066 (    4)
  SS BOND              : angle       0.81952 (    8)
  hydrogen bonds       : bond        0.03848 (  611)
  hydrogen bonds       : angle       4.41487 ( 1830)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1384.13 seconds
wall clock time: 24 minutes 44.67 seconds (1484.67 seconds total)