Starting phenix.real_space_refine
on Tue Mar  3 21:59:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f6g_31479/03_2026/7f6g_31479.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f6g_31479/03_2026/7f6g_31479.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f6g_31479/03_2026/7f6g_31479.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f6g_31479/03_2026/7f6g_31479.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f6g_31479/03_2026/7f6g_31479.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f6g_31479/03_2026/7f6g_31479.map"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      52      5.16       5
     C    5631      2.51       5
     N    1451      2.21       5
     O    1563      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8697
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2520
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 310, 2520
          Classifications: {'peptide': 310}
          Link IDs: {'PTRANS': 12, 'TRANS': 297}
    Chain: "L"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 72
          Classifications: {'peptide': 8}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 6}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'SAR:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 2890
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 349, 2890
          Classifications: {'peptide': 349}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 337}
    Chain: "C"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "D"
      Number of atoms: 433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 433
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "A"
      Number of atoms: 182
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 182
          Unusual residues: {'CLR': 6, 'NAG': 1}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.99, per 1000 atoms: 0.23
  Number of scatterers: 8697
  At special positions: 0
  Unit cell: (101.4, 100.386, 130.806, 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      52     16.00
     O    1563      8.00
     N    1451      7.00
     C    5631      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  18 " - pdb=" SG  CYS A 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 101 " - pdb=" SG  CYS A 180 " 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
  Links applied
    NAG-ASN
      " NAG A 401 " - " ASN A 176 "
  Time building additional restraints: 0.52
  Conformation dependent library (CDL) restraints added in 227.6 milliseconds
  

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2022

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 10 sheets defined
      50.1% alpha, 16.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 56
      Proline residue:  A  32  - end of helix
      removed outlier: 3.571A  pdb=" N   LEU A  48 " --> pdb=" O   PHE A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 80
      removed outlier: 4.331A  pdb=" N   THR A  80 " --> pdb=" O   CYS A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 90
      removed outlier: 3.683A  pdb=" N   TRP A  84 " --> pdb=" O   THR A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 132
      removed outlier: 3.618A  pdb=" N   ALA A 106 " --> pdb=" O   LYS A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 140
      removed outlier: 4.320A  pdb=" N   ARG A 139 " --> pdb=" O   LYS A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 167
      Proline residue:  A 162  - end of helix
    Processing helix  chain 'A' and resid 189 through 202
      removed outlier: 3.807A  pdb=" N   LEU A 195 " --> pdb=" O   LEU A 191 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLY A 196 " --> pdb=" O   PRO A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 230
    Processing helix  chain 'A' and resid 234 through 269
      removed outlier: 3.635A  pdb=" N   ILE A 238 " --> pdb=" O   ARG A 234 " (cutoff:3.500A)
      Proline residue:  A 255  - end of helix
    Processing helix  chain 'A' and resid 273 through 292
      removed outlier: 4.048A  pdb=" N   ILE A 279 " --> pdb=" O   ARG A 275 " (cutoff:3.500A)
      Proline residue:  A 285  - end of helix
    Processing helix  chain 'A' and resid 292 through 302
      Proline residue:  A 299  - end of helix
    Processing helix  chain 'A' and resid 306 through 320
      removed outlier: 3.659A  pdb=" N   LYS A 310 " --> pdb=" O   GLY A 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 12 through 36
      removed outlier: 3.747A  pdb=" N   LYS B  16 " --> pdb=" O   SER B  12 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   GLU B  17 " --> pdb=" O   GLU B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 63
      removed outlier: 3.526A  pdb=" N   MET B  59 " --> pdb=" O   PHE B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 97
      removed outlier: 3.797A  pdb=" N   GLY B  74 " --> pdb=" O   GLU B  70 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   PHE B  75 " --> pdb=" O   ASP B  71 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   THR B  76 " --> pdb=" O   LYS B  72 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   LYS B  77 " --> pdb=" O   ARG B  73 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   LEU B  78 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ASP B  95 " --> pdb=" O   ILE B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 116
      removed outlier: 4.267A  pdb=" N   LYS B 107 " --> pdb=" O   TYR B 103 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   ALA B 108 " --> pdb=" O   GLU B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 138
      removed outlier: 3.547A  pdb=" N   ALA B 131 " --> pdb=" O   PRO B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 147
    Processing helix  chain 'B' and resid 156 through 163
    Processing helix  chain 'B' and resid 163 through 169
    Processing helix  chain 'B' and resid 175 through 182
    Processing helix  chain 'B' and resid 212 through 217
      removed outlier: 4.227A  pdb=" N   TRP B 216 " --> pdb=" O   GLU B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 218 through 221
    Processing helix  chain 'B' and resid 233 through 235
      No H-bonds generated for 'chain 'B' and resid 233 through 235'
    Processing helix  chain 'B' and resid 247 through 261
      removed outlier: 3.537A  pdb=" N   TYR B 261 " --> pdb=" O   THR B 257 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 267
      removed outlier: 4.415A  pdb=" N   ASN B 266 " --> pdb=" O   TRP B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 283
    Processing helix  chain 'B' and resid 301 through 316
      removed outlier: 3.736A  pdb=" N   ALA B 305 " --> pdb=" O   ASP B 301 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ARG B 306 " --> pdb=" O   ALA B 302 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU B 316 " --> pdb=" O   MET B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 335 through 356
    Processing helix  chain 'C' and resid 4 through 25
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'C' and resid 35 through 37
      No H-bonds generated for 'chain 'C' and resid 35 through 37'
    Processing helix  chain 'D' and resid 9 through 24
      removed outlier: 4.100A  pdb=" N   ASN D  24 " --> pdb=" O   LYS D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 44
    Processing helix  chain 'D' and resid 55 through 59
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14
      removed outlier: 6.471A  pdb=" N   LYS A  12 " --> pdb=" O   PHE A 171 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 190 through 195
      removed outlier: 3.509A  pdb=" N   ILE B 190 " --> pdb=" O   ASP B 205 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   LEU B  40 " --> pdb=" O   ARG B 202 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   VAL B 204 " --> pdb=" O   LEU B  40 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   LEU B  42 " --> pdb=" O   VAL B 204 " (cutoff:3.500A)
      removed outlier: 10.096A  pdb=" N   SER B 225 " --> pdb=" O   GLU B  39 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   LYS B  41 " --> pdb=" O   SER B 225 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   MET B 227 " --> pdb=" O   LYS B  41 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   LEU B  43 " --> pdb=" O   MET B 227 " (cutoff:3.500A)
      removed outlier: 7.663A  pdb=" N   LEU B 229 " --> pdb=" O   LEU B  43 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   LEU B  45 " --> pdb=" O   LEU B 229 " (cutoff:3.500A)
      removed outlier: 8.850A  pdb=" N   ALA B 231 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   ILE B 226 " --> pdb=" O   ILE B 270 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   PHE B 272 " --> pdb=" O   ILE B 226 " (cutoff:3.500A)
      removed outlier: 6.040A  pdb=" N   PHE B 228 " --> pdb=" O   PHE B 272 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   ASN B 274 " --> pdb=" O   PHE B 228 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   VAL B 230 " --> pdb=" O   ASN B 274 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 238 through 239
      removed outlier: 3.543A  pdb=" N   LEU B 239 " --> pdb=" O   GLU B 245 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   GLU B 245 " --> pdb=" O   LEU B 239 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 47 through 51
      removed outlier: 3.512A  pdb=" N   ILE C 338 " --> pdb=" O   ARG C  49 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 63
      removed outlier: 3.643A  pdb=" N   ALA C  60 " --> pdb=" O   ALA C  73 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   HIS C  91 " --> pdb=" O   ILE C  81 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   ASP C  83 " --> pdb=" O   LYS C  89 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   LYS C  89 " --> pdb=" O   ASP C  83 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.860A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 4.989A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.066A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   ASN C 125 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   VAL C 135 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 146 through 151
      removed outlier: 6.666A  pdb=" N   CYS C 166 " --> pdb=" O   THR C 179 " (cutoff:3.500A)
      removed outlier: 4.706A  pdb=" N   THR C 179 " --> pdb=" O   CYS C 166 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   LEU C 168 " --> pdb=" O   THR C 177 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 187 through 192
      removed outlier: 3.785A  pdb=" N   GLN C 220 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.390A  pdb=" N   CYS C 250 " --> pdb=" O   THR C 263 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   THR C 263 " --> pdb=" O   CYS C 250 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   LEU C 252 " --> pdb=" O   LEU C 261 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLN C 259 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 273 through 278
      removed outlier: 3.671A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   CYS C 294 " --> pdb=" O   VAL C 307 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   VAL C 307 " --> pdb=" O   CYS C 294 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   VAL C 296 " --> pdb=" O   ALA C 305 " (cutoff:3.500A)

    441 hydrogen bonds defined for protein.
    1284 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: 1.33

  Time building geometry restraints manager: 0.65 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2431
        1.34 -     1.46: 1762
        1.46 -     1.58: 4626
        1.58 -     1.70: 0
        1.70 -     1.83: 77
  Bond restraints: 8896
  Sorted by residual:
  bond pdb=" C10 CLR A 405 "
       pdb=" C5  CLR A 405 "
    ideal  model  delta    sigma   weight residual
    1.519  1.386  0.133 2.00e-02 2.50e+03 4.41e+01
  bond pdb=" C4  CLR A 405 "
       pdb=" C5  CLR A 405 "
    ideal  model  delta    sigma   weight residual
    1.506  1.380  0.126 2.00e-02 2.50e+03 3.96e+01
  bond pdb=" C10 CLR A 404 "
       pdb=" C5  CLR A 404 "
    ideal  model  delta    sigma   weight residual
    1.519  1.403  0.116 2.00e-02 2.50e+03 3.35e+01
  bond pdb=" C10 CLR A 402 "
       pdb=" C5  CLR A 402 "
    ideal  model  delta    sigma   weight residual
    1.519  1.404  0.115 2.00e-02 2.50e+03 3.32e+01
  bond pdb=" C10 CLR A 406 "
       pdb=" C5  CLR A 406 "
    ideal  model  delta    sigma   weight residual
    1.519  1.404  0.115 2.00e-02 2.50e+03 3.31e+01
  ... (remaining 8891 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 10955
        1.63 -     3.26: 964
        3.26 -     4.90: 118
        4.90 -     6.53: 40
        6.53 -     8.16: 9
  Bond angle restraints: 12086
  Sorted by residual:
  angle pdb=" CA  GLY A  97 "
        pdb=" C   GLY A  97 "
        pdb=" O   GLY A  97 "
      ideal   model   delta    sigma   weight residual
     122.23  118.06    4.17 6.90e-01 2.10e+00 3.65e+01
  angle pdb=" C   LYS A 232 "
        pdb=" CA  LYS A 232 "
        pdb=" CB  LYS A 232 "
      ideal   model   delta    sigma   weight residual
     110.71  115.64   -4.93 9.40e-01 1.13e+00 2.75e+01
  angle pdb=" CA  LYS A 232 "
        pdb=" C   LYS A 232 "
        pdb=" N   PRO A 233 "
      ideal   model   delta    sigma   weight residual
     118.16  121.29   -3.13 7.00e-01 2.04e+00 2.00e+01
  angle pdb=" CA  VAL B 184 "
        pdb=" C   VAL B 184 "
        pdb=" N   PRO B 185 "
      ideal   model   delta    sigma   weight residual
     119.30  122.77   -3.47 8.10e-01 1.52e+00 1.83e+01
  angle pdb=" N   LEU B 358 "
        pdb=" CA  LEU B 358 "
        pdb=" C   LEU B 358 "
      ideal   model   delta    sigma   weight residual
     112.45  106.63    5.82 1.39e+00 5.18e-01 1.75e+01
  ... (remaining 12081 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.68: 5309
       23.68 -    47.35: 276
       47.35 -    71.03: 32
       71.03 -    94.71: 8
       94.71 -   118.39: 2
  Dihedral angle restraints: 5627
    sinusoidal: 2505
      harmonic: 3122
  Sorted by residual:
  dihedral pdb=" CA  SER C 227 "
           pdb=" C   SER C 227 "
           pdb=" N   ASP C 228 "
           pdb=" CA  ASP C 228 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.54  -20.46     0      5.00e+00 4.00e-02 1.67e+01
  dihedral pdb=" C10 CLR A 405 "
           pdb=" C1  CLR A 405 "
           pdb=" C2  CLR A 405 "
           pdb=" C3  CLR A 405 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -56.83   61.56 -118.39     1      3.00e+01 1.11e-03 1.57e+01
  dihedral pdb=" CA  PHE C 222 "
           pdb=" C   PHE C 222 "
           pdb=" N   THR C 223 "
           pdb=" CA  THR C 223 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.25  -19.75     0      5.00e+00 4.00e-02 1.56e+01
  ... (remaining 5624 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.097: 1190
       0.097 -    0.195: 157
       0.195 -    0.292: 18
       0.292 -    0.389: 9
       0.389 -    0.487: 11
  Chirality restraints: 1385
  Sorted by residual:
  chirality pdb=" C14 CLR A 402 "
            pdb=" C13 CLR A 402 "
            pdb=" C15 CLR A 402 "
            pdb=" C8  CLR A 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.80    0.49 2.00e-01 2.50e+01 5.92e+00
  chirality pdb=" C14 CLR A 405 "
            pdb=" C13 CLR A 405 "
            pdb=" C15 CLR A 405 "
            pdb=" C8  CLR A 405 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.79    0.47 2.00e-01 2.50e+01 5.51e+00
  chirality pdb=" C14 CLR A 403 "
            pdb=" C13 CLR A 403 "
            pdb=" C15 CLR A 403 "
            pdb=" C8  CLR A 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.78    0.47 2.00e-01 2.50e+01 5.41e+00
  ... (remaining 1382 not shown)

  Planarity restraints: 1496
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 161 "    0.034 5.00e-02 4.00e+02   5.14e-02 4.22e+00
        pdb=" N   PRO A 162 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO A 162 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 162 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B  62 "    0.010 2.00e-02 2.50e+03   2.01e-02 4.02e+00
        pdb=" C   ILE B  62 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   ILE B  62 "    0.013 2.00e-02 2.50e+03
        pdb=" N   HIS B  63 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR C 223 "    0.009 2.00e-02 2.50e+03   1.90e-02 3.62e+00
        pdb=" C   THR C 223 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   THR C 223 "    0.012 2.00e-02 2.50e+03
        pdb=" N   GLY C 224 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1493 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 566
        2.74 -     3.28: 8622
        3.28 -     3.82: 13616
        3.82 -     4.36: 17810
        4.36 -     4.90: 29513
  Nonbonded interactions: 70127
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 161 "
            pdb=" OD1 ASP C 163 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O   SER C  67 "
            pdb=" OG  SER C  67 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" NZ  LYS A 102 "
            pdb=" O   ILE A 164 "
     model   vdw
     2.335 3.120
  nonbonded pdb=" OD2 ASP B 236 "
            pdb=" NZ  LYS B 282 "
     model   vdw
     2.342 3.120
  nonbonded pdb=" O   ASP A 278 "
            pdb=" OG1 THR A 282 "
     model   vdw
     2.355 3.040
  ... (remaining 70122 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.790
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
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      :  0.009   0.133   8899  Z= 0.562
  Angle     :  0.976   8.160  12093  Z= 0.646
  Chirality :  0.080   0.487   1385
  Planarity :  0.004   0.051   1495
  Dihedral  : 13.899 118.386   3599
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  2.59 %
    Favored  : 96.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.57 (0.25), residues: 1050
  helix:  0.14 (0.23), residues: 474
  sheet:  0.21 (0.38), residues: 190
  loop : -1.23 (0.28), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 167 
 TYR   0.012   0.001   TYR B  80 
 PHE   0.012   0.001   PHE A 110 
 TRP   0.011   0.001   TRP C  82 
 HIS   0.003   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00878 ( 8896)
  covalent geometry    : angle       0.97555 (12086)
  SS BOND              : bond        0.00147 (    2)
  SS BOND              : angle       1.72357 (    4)
  hydrogen bonds       : bond        0.25446 (  441)
  hydrogen bonds       : angle       7.17995 ( 1284)
  link_NAG-ASN         : bond        0.00230 (    1)
  link_NAG-ASN         : angle       1.05535 (    3)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 151
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LEU cc_start: 0.7343 (tt) cc_final: 0.7106 (tt)
REVERT: A   99 TYR cc_start: 0.6238 (m-80) cc_final: 0.5510 (m-80)
REVERT: B  265 GLN cc_start: 0.7808 (pt0) cc_final: 0.7555 (pt0)
REVERT: B  303 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7776 (tm-30)
REVERT: C   19 ARG cc_start: 0.7431 (ttp-110) cc_final: 0.7226 (ttm110)
REVERT: C  247 ASP cc_start: 0.7316 (m-30) cc_final: 0.7008 (m-30)
REVERT: C  258 ASP cc_start: 0.7898 (t0) cc_final: 0.6964 (t0)
  outliers start: 6
  outliers final: 4
  residues processed: 154
  average time/residue: 0.6692
  time to fit residues: 108.5976
Evaluate side-chains
  108 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  281 ASP
Chi-restraints excluded: chain B residue   90 MET
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain B residue  115 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 174 ASN
** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  63 HIS
B  82 ASN
B  88 GLN
B 106 ASN
B 162 ASN
B 176 GLN
B 287 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.172247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.115050 restraints weight = 9436.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 2.79
r_work: 0.3082 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.1494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8899  Z= 0.185
  Angle     :  0.613   7.130  12093  Z= 0.324
  Chirality :  0.045   0.205   1385
  Planarity :  0.005   0.052   1495
  Dihedral  :  8.028  73.023   1591
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 10.78 %
    Favored  : 86.42 %
  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:  0.33 (0.25), residues: 1050
  helix:  1.33 (0.23), residues: 482
  sheet:  0.26 (0.37), residues: 185
  loop : -1.22 (0.29), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L   2 
 TYR   0.014   0.001   TYR A 312 
 PHE   0.014   0.002   PHE B 255 
 TRP   0.015   0.001   TRP C  82 
 HIS   0.013   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 8896)
  covalent geometry    : angle       0.61216 (12086)
  SS BOND              : bond        0.00336 (    2)
  SS BOND              : angle       1.76931 (    4)
  hydrogen bonds       : bond        0.06557 (  441)
  hydrogen bonds       : angle       4.66283 ( 1284)
  link_NAG-ASN         : bond        0.00014 (    1)
  link_NAG-ASN         : angle       0.93054 (    3)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 SER cc_start: 0.8388 (m) cc_final: 0.8110 (p)
REVERT: B  105 HIS cc_start: 0.4959 (OUTLIER) cc_final: 0.4431 (m90)
REVERT: B  234 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8032 (mm-30)
REVERT: B  237 GLN cc_start: 0.7132 (mt0) cc_final: 0.6779 (mt0)
REVERT: B  287 HIS cc_start: 0.7540 (m-70) cc_final: 0.7062 (m90)
REVERT: B  299 GLN cc_start: 0.7921 (tt0) cc_final: 0.7156 (tm-30)
REVERT: B  303 GLN cc_start: 0.7324 (tm-30) cc_final: 0.6886 (tm-30)
REVERT: B  333 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7505 (t0)
REVERT: C   19 ARG cc_start: 0.7063 (ttp-110) cc_final: 0.6848 (ttm110)
REVERT: C  217 MET cc_start: 0.8703 (ptm) cc_final: 0.8310 (ptp)
REVERT: C  247 ASP cc_start: 0.7743 (m-30) cc_final: 0.7374 (m-30)
REVERT: C  258 ASP cc_start: 0.8269 (t0) cc_final: 0.7337 (t0)
  outliers start: 26
  outliers final: 15
  residues processed: 118
  average time/residue: 0.6251
  time to fit residues: 78.3475
Evaluate side-chains
  106 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain B residue   90 MET
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain B residue  115 GLU
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain B residue  259 ILE
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain C residue   17 GLN
Chi-restraints excluded: chain C residue   33 ILE
Chi-restraints excluded: chain D residue   31 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 73 optimal weight:    0.7980
   chunk 56 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 37 optimal weight:    6.9990
   chunk 76 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 265 GLN
C  88 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.173597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.116316 restraints weight = 9375.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 2.79
r_work: 0.3101 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8899  Z= 0.136
  Angle     :  0.527   7.111  12093  Z= 0.280
  Chirality :  0.043   0.159   1385
  Planarity :  0.004   0.048   1495
  Dihedral  :  7.399  71.596   1589
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 12.18 %
    Favored  : 85.02 %
  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:  0.73 (0.26), residues: 1050
  helix:  1.79 (0.24), residues: 482
  sheet:  0.47 (0.38), residues: 189
  loop : -1.24 (0.29), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  93 
 TYR   0.011   0.001   TYR A 312 
 PHE   0.013   0.001   PHE A 110 
 TRP   0.014   0.001   TRP C  82 
 HIS   0.002   0.001   HIS C 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 8896)
  covalent geometry    : angle       0.52673 (12086)
  SS BOND              : bond        0.00106 (    2)
  SS BOND              : angle       1.38036 (    4)
  hydrogen bonds       : bond        0.05025 (  441)
  hydrogen bonds       : angle       4.26628 ( 1284)
  link_NAG-ASN         : bond        0.00145 (    1)
  link_NAG-ASN         : angle       0.76602 (    3)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 96
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   91 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7593 (pt0)
REVERT: A  281 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7535 (t0)
REVERT: B  105 HIS cc_start: 0.4929 (OUTLIER) cc_final: 0.4426 (m90)
REVERT: B  237 GLN cc_start: 0.7139 (mt0) cc_final: 0.6822 (tt0)
REVERT: B  287 HIS cc_start: 0.7593 (m-70) cc_final: 0.7121 (m90)
REVERT: B  299 GLN cc_start: 0.7898 (tt0) cc_final: 0.7144 (tm-30)
REVERT: B  303 GLN cc_start: 0.7302 (tm-30) cc_final: 0.6926 (tm-30)
REVERT: C  247 ASP cc_start: 0.7746 (m-30) cc_final: 0.7339 (m-30)
REVERT: C  258 ASP cc_start: 0.8220 (t0) cc_final: 0.7270 (t0)
  outliers start: 26
  outliers final: 14
  residues processed: 113
  average time/residue: 0.6372
  time to fit residues: 76.0923
Evaluate side-chains
  106 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  281 ASP
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain B residue  115 GLU
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  259 ILE
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain C residue   17 GLN
Chi-restraints excluded: chain C residue   33 ILE
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  315 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 64 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 81 optimal weight:    0.6980
   chunk 72 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 98 optimal weight:    6.9990
   chunk 67 optimal weight:   10.0000
   chunk 1 optimal weight:    0.5980
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.173665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.118997 restraints weight = 9607.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 2.52
r_work: 0.3130 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.2127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8899  Z= 0.123
  Angle     :  0.514   7.822  12093  Z= 0.270
  Chirality :  0.042   0.134   1385
  Planarity :  0.004   0.047   1495
  Dihedral  :  6.842  68.643   1586
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 13.36 %
    Favored  : 83.30 %
  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:  0.85 (0.26), residues: 1050
  helix:  1.89 (0.24), residues: 483
  sheet:  0.53 (0.38), residues: 187
  loop : -1.20 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  19 
 TYR   0.010   0.001   TYR A  26 
 PHE   0.013   0.001   PHE A 110 
 TRP   0.013   0.001   TRP C  82 
 HIS   0.002   0.000   HIS B 327 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 8896)
  covalent geometry    : angle       0.51365 (12086)
  SS BOND              : bond        0.00125 (    2)
  SS BOND              : angle       1.28978 (    4)
  hydrogen bonds       : bond        0.04446 (  441)
  hydrogen bonds       : angle       4.09810 ( 1284)
  link_NAG-ASN         : bond        0.00166 (    1)
  link_NAG-ASN         : angle       0.74700 (    3)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 97
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   91 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7571 (pt0)
REVERT: A  281 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7488 (t0)
REVERT: B  105 HIS cc_start: 0.4929 (OUTLIER) cc_final: 0.4424 (m90)
REVERT: B  237 GLN cc_start: 0.7200 (mt0) cc_final: 0.6883 (tt0)
REVERT: B  287 HIS cc_start: 0.7698 (m-70) cc_final: 0.7222 (m90)
REVERT: B  299 GLN cc_start: 0.7861 (tt0) cc_final: 0.7103 (tm-30)
REVERT: B  303 GLN cc_start: 0.7292 (tm-30) cc_final: 0.6924 (tm-30)
REVERT: B  333 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7534 (t0)
REVERT: C  247 ASP cc_start: 0.7756 (m-30) cc_final: 0.7341 (m-30)
REVERT: C  258 ASP cc_start: 0.8210 (t0) cc_final: 0.7278 (t0)
  outliers start: 31
  outliers final: 19
  residues processed: 117
  average time/residue: 0.6046
  time to fit residues: 75.1226
Evaluate side-chains
  113 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 91
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  281 ASP
Chi-restraints excluded: chain B residue   94 MET
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain B residue  115 GLU
Chi-restraints excluded: chain B residue  124 PHE
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  259 ILE
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain D residue   31 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 36 optimal weight:    6.9990
   chunk 70 optimal weight:    4.9990
   chunk 34 optimal weight:    0.7980
   chunk 46 optimal weight:    7.9990
   chunk 58 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 19 optimal weight:    0.7980
   chunk 43 optimal weight:    6.9990
   chunk 94 optimal weight:    6.9990
   chunk 32 optimal weight:    0.8980
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
B  58 GLN
C  16 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.169969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.108286 restraints weight = 9572.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 2.52
r_work: 0.3104 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.2188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   8899  Z= 0.192
  Angle     :  0.571   7.378  12093  Z= 0.300
  Chirality :  0.044   0.151   1385
  Planarity :  0.004   0.050   1495
  Dihedral  :  6.976  70.036   1586
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 14.98 %
    Favored  : 81.47 %
  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:  0.65 (0.26), residues: 1050
  helix:  1.69 (0.24), residues: 489
  sheet:  0.27 (0.38), residues: 191
  loop : -1.20 (0.30), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  19 
 TYR   0.013   0.002   TYR A  26 
 PHE   0.014   0.002   PHE A 110 
 TRP   0.015   0.001   TRP C  82 
 HIS   0.004   0.001   HIS B 327 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 8896)
  covalent geometry    : angle       0.56977 (12086)
  SS BOND              : bond        0.00138 (    2)
  SS BOND              : angle       1.76055 (    4)
  hydrogen bonds       : bond        0.05099 (  441)
  hydrogen bonds       : angle       4.19760 ( 1284)
  link_NAG-ASN         : bond        0.00096 (    1)
  link_NAG-ASN         : angle       0.79421 (    3)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 94
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   91 GLU cc_start: 0.8487 (mt-10) cc_final: 0.7707 (pt0)
REVERT: B  105 HIS cc_start: 0.4993 (OUTLIER) cc_final: 0.4532 (m90)
REVERT: B  287 HIS cc_start: 0.7748 (m-70) cc_final: 0.7254 (m90)
REVERT: B  299 GLN cc_start: 0.7941 (tt0) cc_final: 0.7114 (tm-30)
REVERT: B  303 GLN cc_start: 0.7395 (tm-30) cc_final: 0.7056 (tm-30)
REVERT: C  247 ASP cc_start: 0.7891 (m-30) cc_final: 0.7540 (m-30)
REVERT: C  258 ASP cc_start: 0.8362 (t0) cc_final: 0.7408 (t0)
  outliers start: 33
  outliers final: 24
  residues processed: 114
  average time/residue: 0.6395
  time to fit residues: 77.2407
Evaluate side-chains
  112 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 87
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ILE
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain B residue   62 ILE
Chi-restraints excluded: chain B residue   94 MET
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain B residue  115 GLU
Chi-restraints excluded: chain B residue  124 PHE
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  259 ILE
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain C residue   17 GLN
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue  101 MET
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain D residue   31 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 87 optimal weight:    4.9990
   chunk 92 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 44 optimal weight:    7.9990
   chunk 40 optimal weight:   20.0000
   chunk 18 optimal weight:    0.0020
   chunk 46 optimal weight:    9.9990
   chunk 57 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
B 237 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.173983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.117582 restraints weight = 9449.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 2.72
r_work: 0.3119 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.2378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8899  Z= 0.113
  Angle     :  0.495   7.056  12093  Z= 0.261
  Chirality :  0.042   0.165   1385
  Planarity :  0.004   0.048   1495
  Dihedral  :  6.607  69.720   1586
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 15.73 %
    Favored  : 81.36 %
  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:  0.84 (0.26), residues: 1050
  helix:  1.90 (0.24), residues: 489
  sheet:  0.33 (0.38), residues: 192
  loop : -1.17 (0.31), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  19 
 TYR   0.008   0.001   TYR B  80 
 PHE   0.012   0.001   PHE C 199 
 TRP   0.012   0.001   TRP C  82 
 HIS   0.003   0.001   HIS L   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 8896)
  covalent geometry    : angle       0.49469 (12086)
  SS BOND              : bond        0.00060 (    2)
  SS BOND              : angle       1.18386 (    4)
  hydrogen bonds       : bond        0.04089 (  441)
  hydrogen bonds       : angle       3.99531 ( 1284)
  link_NAG-ASN         : bond        0.00147 (    1)
  link_NAG-ASN         : angle       0.82091 (    3)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   91 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7493 (pt0)
REVERT: A  281 ASP cc_start: 0.7439 (m-30) cc_final: 0.7215 (t0)
REVERT: B  105 HIS cc_start: 0.4978 (OUTLIER) cc_final: 0.4539 (m90)
REVERT: B  237 GLN cc_start: 0.7338 (mt0) cc_final: 0.7058 (tt0)
REVERT: B  287 HIS cc_start: 0.7775 (m-70) cc_final: 0.7303 (m90)
REVERT: B  299 GLN cc_start: 0.7829 (tt0) cc_final: 0.7029 (tm-30)
REVERT: B  303 GLN cc_start: 0.7130 (tm-30) cc_final: 0.6699 (tm-30)
REVERT: B  333 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7557 (t0)
REVERT: C  134 ARG cc_start: 0.6550 (mpp-170) cc_final: 0.6199 (mpt-90)
REVERT: C  247 ASP cc_start: 0.7754 (m-30) cc_final: 0.7319 (m-30)
REVERT: C  258 ASP cc_start: 0.8266 (t0) cc_final: 0.7365 (t0)
REVERT: C  325 MET cc_start: 0.8847 (mmt) cc_final: 0.8564 (tpp)
  outliers start: 27
  outliers final: 18
  residues processed: 115
  average time/residue: 0.6738
  time to fit residues: 81.8176
Evaluate side-chains
  116 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  289 CYS
Chi-restraints excluded: chain B residue   87 MET
Chi-restraints excluded: chain B residue   94 MET
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain B residue  115 GLU
Chi-restraints excluded: chain B residue  124 PHE
Chi-restraints excluded: chain B residue  259 ILE
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain C residue   17 GLN
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue  101 MET
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain D residue   31 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 91 optimal weight:    0.5980
   chunk 56 optimal weight:    0.2980
   chunk 97 optimal weight:    4.9990
   chunk 95 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 17 optimal weight:    7.9990
   chunk 3 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   chunk 44 optimal weight:    5.9990
   chunk 83 optimal weight:    0.6980
   chunk 42 optimal weight:   10.0000
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
B 137 ASN
C 176 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.171601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.114787 restraints weight = 9608.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 2.78
r_work: 0.3075 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.2406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8899  Z= 0.154
  Angle     :  0.543   8.499  12093  Z= 0.285
  Chirality :  0.043   0.145   1385
  Planarity :  0.004   0.049   1495
  Dihedral  :  6.720  69.559   1586
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 15.62 %
    Favored  : 80.71 %
  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: 1050
  helix:  1.83 (0.24), residues: 489
  sheet:  0.46 (0.38), residues: 187
  loop : -1.19 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  19 
 TYR   0.015   0.001   TYR A  56 
 PHE   0.014   0.002   PHE A 110 
 TRP   0.015   0.001   TRP C  82 
 HIS   0.003   0.001   HIS A 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 8896)
  covalent geometry    : angle       0.54193 (12086)
  SS BOND              : bond        0.00171 (    2)
  SS BOND              : angle       1.48239 (    4)
  hydrogen bonds       : bond        0.04602 (  441)
  hydrogen bonds       : angle       4.05531 ( 1284)
  link_NAG-ASN         : bond        0.00186 (    1)
  link_NAG-ASN         : angle       0.75699 (    3)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 94
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   91 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7514 (pt0)
REVERT: B  105 HIS cc_start: 0.5023 (OUTLIER) cc_final: 0.4672 (m90)
REVERT: B  237 GLN cc_start: 0.7284 (mt0) cc_final: 0.7045 (tt0)
REVERT: B  287 HIS cc_start: 0.7786 (m-70) cc_final: 0.7313 (m90)
REVERT: B  299 GLN cc_start: 0.7896 (tt0) cc_final: 0.7048 (tm-30)
REVERT: B  303 GLN cc_start: 0.7193 (tm-30) cc_final: 0.6784 (tm-30)
REVERT: C  134 ARG cc_start: 0.6661 (mpp-170) cc_final: 0.6314 (mpp80)
REVERT: C  138 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8044 (mm-30)
REVERT: C  247 ASP cc_start: 0.7778 (m-30) cc_final: 0.7378 (m-30)
REVERT: C  258 ASP cc_start: 0.8237 (t0) cc_final: 0.7383 (t0)
REVERT: C  325 MET cc_start: 0.8890 (mmt) cc_final: 0.8596 (tpp)
  outliers start: 34
  outliers final: 23
  residues processed: 115
  average time/residue: 0.6616
  time to fit residues: 80.4024
Evaluate side-chains
  117 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ILE
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  189 SER
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  289 CYS
Chi-restraints excluded: chain B residue   87 MET
Chi-restraints excluded: chain B residue   94 MET
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  115 GLU
Chi-restraints excluded: chain B residue  124 PHE
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  259 ILE
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain C residue   17 GLN
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue  101 MET
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain D residue   31 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0870
   chunk 79 optimal weight:    3.9990
   chunk 102 optimal weight:    0.8980
   chunk 85 optimal weight:    3.9990
   chunk 90 optimal weight:    0.4980
   chunk 81 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 36 optimal weight:    5.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.6160

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

Flipped N/Q/H residues before XYZ refinement:
B  22 ASN
B 162 ASN
C  88 ASN
C 176 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.173816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.112034 restraints weight = 9464.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 2.56
r_work: 0.3155 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.2513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8899  Z= 0.114
  Angle     :  0.503   7.244  12093  Z= 0.264
  Chirality :  0.042   0.145   1385
  Planarity :  0.004   0.047   1495
  Dihedral  :  6.366  69.014   1582
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 15.84 %
    Favored  : 80.71 %
  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:  0.90 (0.26), residues: 1050
  helix:  1.96 (0.24), residues: 488
  sheet:  0.33 (0.38), residues: 191
  loop : -1.12 (0.31), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  19 
 TYR   0.008   0.001   TYR A  26 
 PHE   0.013   0.001   PHE B  55 
 TRP   0.013   0.001   TRP C  82 
 HIS   0.002   0.001   HIS B 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 8896)
  covalent geometry    : angle       0.50298 (12086)
  SS BOND              : bond        0.00059 (    2)
  SS BOND              : angle       1.13581 (    4)
  hydrogen bonds       : bond        0.04034 (  441)
  hydrogen bonds       : angle       3.95309 ( 1284)
  link_NAG-ASN         : bond        0.00165 (    1)
  link_NAG-ASN         : angle       0.81315 (    3)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 98
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   91 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7679 (pt0)
REVERT: B  105 HIS cc_start: 0.5197 (OUTLIER) cc_final: 0.4919 (m90)
REVERT: B  237 GLN cc_start: 0.7345 (mt0) cc_final: 0.7100 (tt0)
REVERT: B  303 GLN cc_start: 0.7298 (tm-30) cc_final: 0.6913 (tm-30)
REVERT: B  333 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7586 (t0)
REVERT: C  134 ARG cc_start: 0.6715 (mpp-170) cc_final: 0.6338 (mpt-90)
REVERT: C  138 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8207 (mm-30)
REVERT: C  186 ASP cc_start: 0.8712 (m-30) cc_final: 0.8502 (m-30)
REVERT: C  247 ASP cc_start: 0.7850 (m-30) cc_final: 0.7453 (m-30)
REVERT: C  258 ASP cc_start: 0.8355 (t0) cc_final: 0.7520 (t0)
REVERT: C  325 MET cc_start: 0.8972 (mmt) cc_final: 0.8711 (tpp)
  outliers start: 32
  outliers final: 19
  residues processed: 117
  average time/residue: 0.6473
  time to fit residues: 80.1128
Evaluate side-chains
  114 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  189 SER
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  289 CYS
Chi-restraints excluded: chain B residue   94 MET
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  115 GLU
Chi-restraints excluded: chain B residue  124 PHE
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  259 ILE
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain C residue   17 GLN
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue  101 MET
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain D residue   31 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 100 optimal weight:    3.9990
   chunk 88 optimal weight:    3.9990
   chunk 56 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 92 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 43 optimal weight:    7.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
B 287 HIS
C 176 GLN
C 266 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.171201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.114470 restraints weight = 9571.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 2.74
r_work: 0.3078 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.2503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8899  Z= 0.176
  Angle     :  0.568   8.282  12093  Z= 0.297
  Chirality :  0.044   0.182   1385
  Planarity :  0.004   0.049   1495
  Dihedral  :  6.557  68.488   1582
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 16.81 %
    Favored  : 80.06 %
  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:  0.76 (0.26), residues: 1050
  helix:  1.81 (0.24), residues: 488
  sheet:  0.29 (0.38), residues: 191
  loop : -1.16 (0.31), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  19 
 TYR   0.016   0.001   TYR A  56 
 PHE   0.014   0.002   PHE A 110 
 TRP   0.015   0.001   TRP C  82 
 HIS   0.003   0.001   HIS A 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 8896)
  covalent geometry    : angle       0.56739 (12086)
  SS BOND              : bond        0.00172 (    2)
  SS BOND              : angle       1.53450 (    4)
  hydrogen bonds       : bond        0.04655 (  441)
  hydrogen bonds       : angle       4.05642 ( 1284)
  link_NAG-ASN         : bond        0.00166 (    1)
  link_NAG-ASN         : angle       0.78637 (    3)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 93
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   91 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7566 (pt0)
REVERT: B  105 HIS cc_start: 0.5170 (OUTLIER) cc_final: 0.4885 (m90)
REVERT: B  237 GLN cc_start: 0.7238 (mt0) cc_final: 0.6995 (tt0)
REVERT: B  303 GLN cc_start: 0.7193 (tm-30) cc_final: 0.6790 (tm-30)
REVERT: C  134 ARG cc_start: 0.6641 (mpp-170) cc_final: 0.6372 (mpt180)
REVERT: C  138 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8033 (mm-30)
REVERT: C  186 ASP cc_start: 0.8678 (m-30) cc_final: 0.8458 (m-30)
REVERT: C  247 ASP cc_start: 0.7774 (m-30) cc_final: 0.7393 (m-30)
REVERT: C  258 ASP cc_start: 0.8229 (t0) cc_final: 0.7405 (t0)
REVERT: C  325 MET cc_start: 0.8935 (mmt) cc_final: 0.8635 (tpp)
  outliers start: 29
  outliers final: 25
  residues processed: 113
  average time/residue: 0.6205
  time to fit residues: 74.3062
Evaluate side-chains
  120 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 94
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  189 SER
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  289 CYS
Chi-restraints excluded: chain B residue   94 MET
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  124 PHE
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  259 ILE
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain C residue   17 GLN
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue  101 MET
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain D residue   31 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 35 optimal weight:    0.4980
   chunk 18 optimal weight:    0.0970
   chunk 8 optimal weight:    3.9990
   chunk 99 optimal weight:    6.9990
   chunk 95 optimal weight:    6.9990
   chunk 2 optimal weight:    0.7980
   chunk 100 optimal weight:    0.4980
   chunk 80 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   chunk 102 optimal weight:    0.0870
   chunk 46 optimal weight:   10.0000
   overall best weight:    0.3956

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.175698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.114025 restraints weight = 9442.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 2.53
r_work: 0.3177 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work: 0.3027 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.2660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8899  Z= 0.108
  Angle     :  0.515   8.230  12093  Z= 0.270
  Chirality :  0.041   0.157   1385
  Planarity :  0.004   0.045   1495
  Dihedral  :  5.977  59.992   1579
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 17.46 %
    Favored  : 80.06 %
  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:  0.97 (0.26), residues: 1050
  helix:  2.03 (0.24), residues: 488
  sheet:  0.44 (0.38), residues: 189
  loop : -1.15 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C  19 
 TYR   0.008   0.001   TYR B  80 
 PHE   0.013   0.001   PHE B  55 
 TRP   0.013   0.001   TRP A 219 
 HIS   0.002   0.000   HIS L   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 8896)
  covalent geometry    : angle       0.51460 (12086)
  SS BOND              : bond        0.00119 (    2)
  SS BOND              : angle       0.95341 (    4)
  hydrogen bonds       : bond        0.03784 (  441)
  hydrogen bonds       : angle       3.90694 ( 1284)
  link_NAG-ASN         : bond        0.00141 (    1)
  link_NAG-ASN         : angle       0.84281 (    3)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   91 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7673 (pt0)
REVERT: B  105 HIS cc_start: 0.5130 (OUTLIER) cc_final: 0.4872 (m90)
REVERT: B  237 GLN cc_start: 0.7307 (mt0) cc_final: 0.7075 (tt0)
REVERT: B  299 GLN cc_start: 0.7552 (tt0) cc_final: 0.6950 (tp40)
REVERT: B  303 GLN cc_start: 0.7277 (tm-30) cc_final: 0.6888 (tm-30)
REVERT: B  333 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7602 (t0)
REVERT: C  134 ARG cc_start: 0.6715 (mpp-170) cc_final: 0.6363 (mpt-90)
REVERT: C  138 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8246 (mt-10)
REVERT: C  186 ASP cc_start: 0.8666 (m-30) cc_final: 0.8442 (m-30)
REVERT: C  247 ASP cc_start: 0.7862 (m-30) cc_final: 0.7446 (m-30)
REVERT: C  258 ASP cc_start: 0.8338 (t0) cc_final: 0.7558 (t0)
  outliers start: 23
  outliers final: 14
  residues processed: 118
  average time/residue: 0.6100
  time to fit residues: 76.3372
Evaluate side-chains
  112 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  189 SER
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  289 CYS
Chi-restraints excluded: chain B residue   94 MET
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  124 PHE
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  259 ILE
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain D residue   31 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 101 optimal weight:    0.8980
   chunk 4 optimal weight:    5.9990
   chunk 67 optimal weight:   10.0000
   chunk 75 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 87 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 44 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
** A 267 GLN ** 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 = 0.3975 r_free = 0.3975 target = 0.171256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.108935 restraints weight = 9530.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 2.54
r_work: 0.3118 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.2602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8899  Z= 0.175
  Angle     :  0.577   8.131  12093  Z= 0.302
  Chirality :  0.044   0.157   1385
  Planarity :  0.004   0.045   1495
  Dihedral  :  6.100  54.191   1579
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 18.21 %
    Favored  : 79.63 %
  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:  0.87 (0.26), residues: 1050
  helix:  1.93 (0.24), residues: 482
  sheet:  0.31 (0.38), residues: 191
  loop : -1.09 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  19 
 TYR   0.020   0.001   TYR A  56 
 PHE   0.014   0.002   PHE A 110 
 TRP   0.015   0.001   TRP C  82 
 HIS   0.003   0.001   HIS A 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 8896)
  covalent geometry    : angle       0.57610 (12086)
  SS BOND              : bond        0.00160 (    2)
  SS BOND              : angle       1.52399 (    4)
  hydrogen bonds       : bond        0.04622 (  441)
  hydrogen bonds       : angle       4.04954 ( 1284)
  link_NAG-ASN         : bond        0.00200 (    1)
  link_NAG-ASN         : angle       0.76180 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3283.88 seconds
wall clock time: 56 minutes 32.84 seconds (3392.84 seconds total)