Starting phenix.real_space_refine
on Thu Jan 23 02:25:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v24_42897/01_2025/8v24_42897_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v24_42897/01_2025/8v24_42897.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8v24_42897/01_2025/8v24_42897.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v24_42897/01_2025/8v24_42897.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v24_42897/01_2025/8v24_42897_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v24_42897/01_2025/8v24_42897_trim.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.064
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: 7
    Type Number    sf(0)   Gaussians
     Zn      4      6.06       5
     P       4      5.49       5
     S      68      5.16       5
     C    6310      2.51       5
     N    1764      2.21       5
     O    1901      1.98       5
     H    9601      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 19652
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 5165
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 327, 5165
          Classifications: {'peptide': 327}
          Link IDs: {'PTRANS': 4, 'TRANS': 322}
    Chain: "B"
      Number of atoms: 4595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 301, 4595
          Classifications: {'peptide': 301}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 288}
    Chain: "C"
      Number of atoms: 5167
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 323, 5167
          Classifications: {'peptide': 323}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 318}
    Chain: "D"
      Number of atoms: 4609
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 302, 4609
          Classifications: {'peptide': 302}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 289}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 57
          Unusual residues: {' ZN': 1, '24G': 1, 'ACT': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 57
          Unusual residues: {' ZN': 1, '24G': 1, 'ACT': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   4669  SG  CYS A 357      55.527  54.008  44.022  1.00 66.24           S
  ATOM   4719  SG  CYS A 360      52.507  56.006  45.208  1.00 63.26           S
  ATOM   4897  SG  CYS A 371      53.294  55.609  41.513  1.00 60.78           S
  ATOM   4933  SG  CYS A 374      55.482  57.829  43.701  1.00 62.49           S
  ATOM  14412  SG  CYS C 357      34.062  52.227  59.516  1.00 59.78           S
  ATOM  14462  SG  CYS C 360      37.401  54.248  59.253  1.00 58.85           S
  ATOM  14640  SG  CYS C 371      36.302  52.894  62.486  1.00 56.68           S
  ATOM  14676  SG  CYS C 374      34.343  55.749  60.926  1.00 58.27           S

  Time building chain proxies: 11.36, per 1000 atoms: 0.58
  Number of scatterers: 19652
  At special positions: 0
  Unit cell: (90.78, 108.936, 111.072, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      4     29.99
     S      68     16.00
     P       4     15.00
     O    1901      8.00
     N    1764      7.00
     C    6310      6.00
     H    9601      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 7.52
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 401 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS A 371 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS A 357 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS A 360 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS A 374 "
      pdb="  ZN B 403 "
        pdb="ZN    ZN B 403 " - pdb=" NE2 HIS B 238 "
        pdb="ZN    ZN B 403 " - pdb=" NE2 HIS B  79 "
      pdb="  ZN C 401 "
        pdb="ZN    ZN C 401 " - pdb=" SG  CYS C 371 "
        pdb="ZN    ZN C 401 " - pdb=" SG  CYS C 374 "
        pdb="ZN    ZN C 401 " - pdb=" SG  CYS C 360 "
        pdb="ZN    ZN C 401 " - pdb=" SG  CYS C 357 "
      pdb="  ZN D 403 "
        pdb="ZN    ZN D 403 " - pdb=" NE2 HIS D 238 "
        pdb="ZN    ZN D 403 " - pdb=" NE2 HIS D  79 "
      Number of angles added : 12


  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2358

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 13 sheets defined
      53.3% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 69 through 83
    Processing helix  chain 'A' and resid 84 through 98
    Processing helix  chain 'A' and resid 102 through 121
    Processing helix  chain 'A' and resid 122 through 131
    Processing helix  chain 'A' and resid 139 through 154
    Processing helix  chain 'A' and resid 156 through 170
    Processing helix  chain 'A' and resid 176 through 192
    Processing helix  chain 'A' and resid 195 through 210
    Processing helix  chain 'A' and resid 213 through 228
      removed outlier: 3.755A  pdb=" N   SER A 217 " --> pdb=" O   SER A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 239
      removed outlier: 3.818A  pdb=" N   ARG A 239 " --> pdb=" O   GLU A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 244
    Processing helix  chain 'A' and resid 248 through 263
      removed outlier: 3.863A  pdb=" N   LEU A 252 " --> pdb=" O   VAL A 248 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   GLU A 253 " --> pdb=" O   SER A 249 " (cutoff:3.500A)
      removed outlier: 5.025A  pdb=" N   MET A 254 " --> pdb=" O   GLU A 250 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   THR A 257 " --> pdb=" O   GLU A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 281 through 297
      removed outlier: 3.625A  pdb=" N   GLU A 285 " --> pdb=" O   GLY A 281 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ALA A 294 " --> pdb=" O   ASP A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 301
      No H-bonds generated for 'chain 'A' and resid 299 through 301'
    Processing helix  chain 'A' and resid 302 through 312
      removed outlier: 3.620A  pdb=" N   ARG A 311 " --> pdb=" O   ARG A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 328
      removed outlier: 4.268A  pdb=" N   LYS A 320 " --> pdb=" O   ARG A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 341
    Processing helix  chain 'A' and resid 344 through 348
    Processing helix  chain 'B' and resid 53 through 55
      No H-bonds generated for 'chain 'B' and resid 53 through 55'
    Processing helix  chain 'B' and resid 79 through 88
    Processing helix  chain 'B' and resid 108 through 119
    Processing helix  chain 'B' and resid 178 through 186
    Processing helix  chain 'B' and resid 197 through 204
      removed outlier: 3.609A  pdb=" N   SER B 203 " --> pdb=" O   GLU B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 215
      removed outlier: 3.884A  pdb=" N   ALA B 215 " --> pdb=" O   PHE B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 248
      removed outlier: 3.548A  pdb=" N   ARG B 237 " --> pdb=" O   ASP B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 251
      No H-bonds generated for 'chain 'B' and resid 249 through 251'
    Processing helix  chain 'B' and resid 264 through 278
      removed outlier: 3.606A  pdb=" N   ASN B 268 " --> pdb=" O   GLY B 264 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ASN B 269 " --> pdb=" O   HIS B 265 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 68 through 72
      removed outlier: 3.667A  pdb=" N   HIS C  72 " --> pdb=" O   THR C  68 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 68 through 72'
    Processing helix  chain 'C' and resid 74 through 83
    Processing helix  chain 'C' and resid 84 through 98
      removed outlier: 3.592A  pdb=" N   ARG C  90 " --> pdb=" O   ASP C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 121
    Processing helix  chain 'C' and resid 122 through 131
      removed outlier: 3.557A  pdb=" N   ASP C 128 " --> pdb=" O   ASP C 124 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 139 through 154
    Processing helix  chain 'C' and resid 156 through 170
      removed outlier: 3.502A  pdb=" N   ALA C 160 " --> pdb=" O   GLU C 156 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ASP C 162 " --> pdb=" O   GLN C 158 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 172 through 174
      No H-bonds generated for 'chain 'C' and resid 172 through 174'
    Processing helix  chain 'C' and resid 175 through 191
    Processing helix  chain 'C' and resid 195 through 210
    Processing helix  chain 'C' and resid 213 through 228
      removed outlier: 3.809A  pdb=" N   SER C 217 " --> pdb=" O   SER C 213 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 229 through 238
    Processing helix  chain 'C' and resid 238 through 244
      removed outlier: 4.453A  pdb=" N   SER C 242 " --> pdb=" O   GLN C 238 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 247 through 261
      removed outlier: 3.995A  pdb=" N   THR C 251 " --> pdb=" O   LEU C 247 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   GLU C 253 " --> pdb=" O   SER C 249 " (cutoff:3.500A)
      removed outlier: 4.561A  pdb=" N   MET C 254 " --> pdb=" O   GLU C 250 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   THR C 257 " --> pdb=" O   GLU C 253 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 264 through 278
    Processing helix  chain 'C' and resid 281 through 312
      removed outlier: 7.723A  pdb=" N   SER C 298 " --> pdb=" O   ALA C 294 " (cutoff:3.500A)
      removed outlier: 9.211A  pdb=" N   GLU C 299 " --> pdb=" O   ARG C 295 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   ALA C 300 " --> pdb=" O   ASP C 296 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ALA C 301 " --> pdb=" O   GLY C 297 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 314 through 328
      removed outlier: 3.602A  pdb=" N   GLU C 328 " --> pdb=" O   TYR C 324 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 332 through 352
      removed outlier: 3.761A  pdb=" N   GLU C 347 " --> pdb=" O   ASP C 343 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 77 through 88
    Processing helix  chain 'D' and resid 108 through 119
    Processing helix  chain 'D' and resid 178 through 186
    Processing helix  chain 'D' and resid 198 through 205
    Processing helix  chain 'D' and resid 211 through 215
      removed outlier: 4.035A  pdb=" N   ALA D 215 " --> pdb=" O   PHE D 212 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 233 through 248
      removed outlier: 3.603A  pdb=" N   ARG D 237 " --> pdb=" O   ASP D 233 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 249 through 251
      No H-bonds generated for 'chain 'D' and resid 249 through 251'
    Processing helix  chain 'D' and resid 264 through 278
    Processing sheet with id=AA1, first strand: chain 'A' and resid 363 through 364
    Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 16
      removed outlier: 3.605A  pdb=" N   VAL B  48 " --> pdb=" O   ARG B  41 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 57 through 59
      removed outlier: 5.380A  pdb=" N   VAL B  57 " --> pdb=" O   VAL B  67 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   VAL B  67 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ASP B  59 " --> pdb=" O   CYS B  65 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 136 through 139
      removed outlier: 6.355A  pdb=" N   SER B 154 " --> pdb=" O   PHE B 258 " (cutoff:3.500A)
      removed outlier: 7.706A  pdb=" N   ALA B 260 " --> pdb=" O   SER B 154 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   ASP B 156 " --> pdb=" O   ALA B 260 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   TYR B 173 " --> pdb=" O   PHE B 157 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 136 through 139
      removed outlier: 7.901A  pdb=" N   ALA B 257 " --> pdb=" O   ILE B 132 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 194
    Processing sheet with id=AA7, first strand: chain 'C' and resid 363 through 364
    Processing sheet with id=AA8, first strand: chain 'D' and resid 5 through 7
    Processing sheet with id=AA9, first strand: chain 'D' and resid 11 through 16
      removed outlier: 3.663A  pdb=" N   ARG D  41 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 57 through 59
      removed outlier: 5.552A  pdb=" N   VAL D  57 " --> pdb=" O   VAL D  67 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   VAL D  67 " --> pdb=" O   VAL D  57 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ASP D  59 " --> pdb=" O   CYS D  65 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 136 through 139
      removed outlier: 6.704A  pdb=" N   SER D 154 " --> pdb=" O   PHE D 258 " (cutoff:3.500A)
      removed outlier: 8.070A  pdb=" N   ALA D 260 " --> pdb=" O   SER D 154 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   ASP D 156 " --> pdb=" O   ALA D 260 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 136 through 139
      removed outlier: 6.366A  pdb=" N   VAL D 130 " --> pdb=" O   ILE D 255 " (cutoff:3.500A)
      removed outlier: 8.264A  pdb=" N   ALA D 257 " --> pdb=" O   VAL D 130 " (cutoff:3.500A)
      removed outlier: 8.798A  pdb=" N   ILE D 132 " --> pdb=" O   ALA D 257 " (cutoff:3.500A)
      removed outlier: 12.012A  pdb=" N   THR D 259 " --> pdb=" O   ILE D 132 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 193 through 194
      removed outlier: 6.574A  pdb=" N   GLY D 193 " --> pdb=" O   VAL D 218 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4

    535 hydrogen bonds defined for protein.
    1539 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: 7.50

  Time building geometry restraints manager: 6.78 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 9577
        1.03 -     1.23: 34
        1.23 -     1.42: 4243
        1.42 -     1.61: 5858
        1.61 -     1.81: 112
  Bond restraints: 19824
  Sorted by residual:
  bond pdb=" N   MET D   1 "
       pdb=" H3  MET D   1 "
    ideal  model  delta    sigma   weight residual
    0.890  0.960 -0.070 2.00e-02 2.50e+03 1.23e+01
  bond pdb=" N   MET B   1 "
       pdb=" H2  MET B   1 "
    ideal  model  delta    sigma   weight residual
    0.890  0.960 -0.070 2.00e-02 2.50e+03 1.22e+01
  bond pdb=" N   MET B   1 "
       pdb=" H3  MET B   1 "
    ideal  model  delta    sigma   weight residual
    0.890  0.960 -0.070 2.00e-02 2.50e+03 1.21e+01
  bond pdb=" N   MET D   1 "
       pdb=" H2  MET D   1 "
    ideal  model  delta    sigma   weight residual
    0.890  0.959 -0.069 2.00e-02 2.50e+03 1.20e+01
  bond pdb=" N   ASN B  45 "
       pdb=" CA  ASN B  45 "
    ideal  model  delta    sigma   weight residual
    1.462  1.493 -0.032 9.50e-03 1.11e+04 1.13e+01
  ... (remaining 19819 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.99: 35544
        6.99 -    13.98: 12
       13.98 -    20.97: 0
       20.97 -    27.96: 0
       27.96 -    34.95: 3
  Bond angle restraints: 35559
  Sorted by residual:
  angle pdb=" C   ASP A 343 "
        pdb=" CA  ASP A 343 "
        pdb=" HA  ASP A 343 "
      ideal   model   delta    sigma   weight residual
     109.00   74.05   34.95 3.00e+00 1.11e-01 1.36e+02
  angle pdb=" N   ASP A 343 "
        pdb=" CA  ASP A 343 "
        pdb=" HA  ASP A 343 "
      ideal   model   delta    sigma   weight residual
     110.00   75.67   34.33 3.00e+00 1.11e-01 1.31e+02
  angle pdb=" CB  ASP A 343 "
        pdb=" CA  ASP A 343 "
        pdb=" HA  ASP A 343 "
      ideal   model   delta    sigma   weight residual
     109.00   75.31   33.69 3.00e+00 1.11e-01 1.26e+02
  angle pdb=" C   PRO D  46 "
        pdb=" CA  PRO D  46 "
        pdb=" CB  PRO D  46 "
      ideal   model   delta    sigma   weight residual
     110.92  122.35  -11.43 1.22e+00 6.72e-01 8.77e+01
  angle pdb=" N   PRO D  46 "
        pdb=" CA  PRO D  46 "
        pdb=" CB  PRO D  46 "
      ideal   model   delta    sigma   weight residual
     103.08   96.05    7.03 9.70e-01 1.06e+00 5.25e+01
  ... (remaining 35554 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.80: 8888
       33.80 -    67.61: 420
       67.61 -   101.41: 54
      101.41 -   135.21: 11
      135.21 -   169.02: 5
  Dihedral angle restraints: 9378
    sinusoidal: 5164
      harmonic: 4214
  Sorted by residual:
  dihedral pdb=" CA  ARG A 342 "
           pdb=" C   ARG A 342 "
           pdb=" N   ASP A 343 "
           pdb=" CA  ASP A 343 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.99   24.01     0      5.00e+00 4.00e-02 2.31e+01
  dihedral pdb=" C1  24G B 401 "
           pdb=" C6  24G B 401 "
           pdb=" C7  24G B 401 "
           pdb=" O8  24G B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -175.79   -6.77 -169.02     1      3.00e+01 1.11e-03 2.11e+01
  dihedral pdb=" O5  24G B 401 "
           pdb=" C6  24G B 401 "
           pdb=" C7  24G B 401 "
           pdb=" O8  24G B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      63.21 -129.86 -166.93     1      3.00e+01 1.11e-03 2.11e+01
  ... (remaining 9375 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 1422
       0.075 -    0.149: 104
       0.149 -    0.224: 5
       0.224 -    0.299: 0
       0.299 -    0.373: 1
  Chirality restraints: 1532
  Sorted by residual:
  chirality pdb=" CA  ASP A 343 "
            pdb=" N   ASP A 343 "
            pdb=" C   ASP A 343 "
            pdb=" CB  ASP A 343 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.48e+00
  chirality pdb=" CA  PHE D  50 "
            pdb=" N   PHE D  50 "
            pdb=" C   PHE D  50 "
            pdb=" CB  PHE D  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CA  ILE B 101 "
            pdb=" N   ILE B 101 "
            pdb=" C   ILE B 101 "
            pdb=" CB  ILE B 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.72e-01
  ... (remaining 1529 not shown)

  Planarity restraints: 2968
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN D  45 "    0.067 2.00e-02 2.50e+03   4.39e-01 2.90e+03
        pdb=" CG  ASN D  45 "    0.009 2.00e-02 2.50e+03
        pdb=" OD1 ASN D  45 "   -0.074 2.00e-02 2.50e+03
        pdb=" ND2 ASN D  45 "    0.001 2.00e-02 2.50e+03
        pdb="HD21 ASN D  45 "   -0.760 2.00e-02 2.50e+03
        pdb="HD22 ASN D  45 "    0.756 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B  45 "   -0.101 2.00e-02 2.50e+03   4.36e-01 2.85e+03
        pdb=" CG  ASN B  45 "    0.002 2.00e-02 2.50e+03
        pdb=" OD1 ASN B  45 "    0.103 2.00e-02 2.50e+03
        pdb=" ND2 ASN B  45 "   -0.000 2.00e-02 2.50e+03
        pdb="HD21 ASN B  45 "    0.746 2.00e-02 2.50e+03
        pdb="HD22 ASN B  45 "   -0.750 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO D  46 "    0.027 2.00e-02 2.50e+03   5.18e-02 2.68e+01
        pdb=" C   PRO D  46 "   -0.090 2.00e-02 2.50e+03
        pdb=" O   PRO D  46 "    0.032 2.00e-02 2.50e+03
        pdb=" N   PRO D  47 "    0.031 2.00e-02 2.50e+03
  ... (remaining 2965 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 1327
        2.20 -     2.80: 40119
        2.80 -     3.40: 54196
        3.40 -     4.00: 70651
        4.00 -     4.60: 110919
  Nonbonded interactions: 277212
  Sorted by model distance:
  nonbonded pdb=" H   ASP A 343 "
            pdb=" HA  ASP A 343 "
     model   vdw
     1.599 1.816
  nonbonded pdb=" HH  TYR D  39 "
            pdb=" OD1 ASN D  81 "
     model   vdw
     1.632 2.450
  nonbonded pdb=" HE  ARG C  80 "
            pdb=" OD1 ASP C 116 "
     model   vdw
     1.632 2.450
  nonbonded pdb=" H   ARG B 190 "
            pdb=" OE2 GLU B 234 "
     model   vdw
     1.633 2.450
  nonbonded pdb=" OD1 ASP D  90 "
            pdb=" HZ2 LYS D 127 "
     model   vdw
     1.635 2.450
  ... (remaining 277207 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 67 through 389 or resid 401))
  selection = (chain 'C' and ((resid 67 and (name N or name CA or name C or name O )) or (resi \ 
d 68 and (name N or name CA or name C or name O or name CB or name OG1 or name C \ 
G2)) or resid 69 through 346 or (resid 347 and (name N or name CA or name C or n \ 
ame O or name CB or name CG or name CD or name OE1 or name OE2)) or resid 348 th \ 
rough 386 or (resid 387 and (name N or name CA or name C or name O or name CB or \ 
 name CG or name OD1 or name OD2)) or (resid 388 and (name N or name CA or name  \ 
C or name O )) or (resid 389 and (name N or name CA or name C or name O or name  \ 
CB or name CG or name CD1 or name CD2)) or resid 401))
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'D' and (resid 1 through 286 or (resid 287 and (name N or name CA or name \ 
 C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ 
E2 or name CZ )) or resid 288 through 301 or resid 401 through 403))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             0.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.270
  Extract box with map and model:          0.690
  Check model and map are aligned:         0.140
  Set scattering table:                    0.180
  Process input model:                     53.380
  Find NCS groups from input model:        0.710
  Set up NCS constraints:                  0.060
  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:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   59.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
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      :  0.004   0.104  10223  Z= 0.272
  Angle     :  0.630  11.426  13797  Z= 0.365
  Chirality :  0.040   0.373   1532
  Planarity :  0.004   0.099   1786
  Dihedral  : 20.509 169.017   3930
  Min Nonbonded Distance : 1.879

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.70 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 22.33 %
    Favored  : 77.19 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.25), residues: 1245
  helix:  1.43 (0.22), residues: 632
  sheet: -1.62 (0.38), residues: 172
  loop : -1.25 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 268 
 HIS   0.006   0.001   HIS B 238 
 PHE   0.042   0.001   PHE D  50 
 TYR   0.011   0.001   TYR C 230 
 ARG   0.002   0.000   ARG A 333 

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 136
  time to evaluate  : 2.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  287 MET cc_start: 0.7947 (mtp) cc_final: 0.7570 (mtt)
  outliers start: 5
  outliers final: 2
  residues processed: 139
  average time/residue: 0.5029
  time to fit residues: 99.7592
Evaluate side-chains
  132 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 130
  time to evaluate  : 1.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain C residue  236 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 97 optimal weight:    0.4980
   chunk 37 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 112 optimal weight:    1.9990
   overall best weight:    1.8988

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

Flipped N/Q/H residues before XYZ refinement:
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 238 HIS ** 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 = 0.3276 r_free = 0.3276 target = 0.124280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.092505 restraints weight = 35145.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.097268 restraints weight = 17448.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.100293 restraints weight = 11368.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.0662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  10223  Z= 0.302
  Angle     :  0.560   9.168  13797  Z= 0.293
  Chirality :  0.041   0.354   1532
  Planarity :  0.005   0.142   1786
  Dihedral  : 14.266 169.453   1526
  Min Nonbonded Distance : 1.847

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.99 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 21.37 %
    Favored  : 77.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.25), residues: 1245
  helix:  1.19 (0.21), residues: 645
  sheet: -1.43 (0.39), residues: 167
  loop : -1.36 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 268 
 HIS   0.010   0.001   HIS B 238 
 PHE   0.012   0.001   PHE D  50 
 TYR   0.010   0.001   TYR A 368 
 ARG   0.003   0.000   ARG A  80 

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 142
  time to evaluate  : 1.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7619 (mp)
REVERT: B  112 VAL cc_start: 0.8464 (OUTLIER) cc_final: 0.8161 (t)
REVERT: B  200 TYR cc_start: 0.8687 (t80) cc_final: 0.8000 (t80)
REVERT: D    9 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7830 (mtm110)
  outliers start: 17
  outliers final: 9
  residues processed: 152
  average time/residue: 0.4778
  time to fit residues: 103.3460
Evaluate side-chains
  142 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 130
  time to evaluate  : 1.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   94 THR
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  183 MET
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  380 ILE
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue    9 ARG
Chi-restraints excluded: chain D residue  175 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 42 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 115 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.126057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.094421 restraints weight = 34732.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.099348 restraints weight = 17031.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.102542 restraints weight = 10960.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.0906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074  10223  Z= 0.183
  Angle     :  0.462   8.704  13797  Z= 0.248
  Chirality :  0.038   0.355   1532
  Planarity :  0.005   0.138   1786
  Dihedral  : 10.010 120.680   1525
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.22 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 21.09 %
    Favored  : 76.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.25), residues: 1245
  helix:  1.45 (0.22), residues: 646
  sheet: -1.23 (0.40), residues: 167
  loop : -1.31 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 268 
 HIS   0.006   0.001   HIS B 238 
 PHE   0.007   0.001   PHE C 271 
 TYR   0.008   0.001   TYR C 230 
 ARG   0.003   0.000   ARG C 342 

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 137
  time to evaluate  : 1.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 MET cc_start: 0.8156 (tpt) cc_final: 0.7717 (tpt)
REVERT: B  112 VAL cc_start: 0.8416 (OUTLIER) cc_final: 0.8106 (t)
REVERT: B  292 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7292 (mt-10)
  outliers start: 21
  outliers final: 14
  residues processed: 154
  average time/residue: 0.4808
  time to fit residues: 105.8686
Evaluate side-chains
  141 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 1.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  146 GLU
Chi-restraints excluded: chain B residue  147 PHE
Chi-restraints excluded: chain B residue  292 GLU
Chi-restraints excluded: chain C residue  210 ASP
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  378 SER
Chi-restraints excluded: chain C residue  380 ILE
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   76 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 88 optimal weight:    7.9990
   chunk 107 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 78 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 111 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 302 GLN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.123208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.092164 restraints weight = 35341.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.096646 restraints weight = 18363.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.099506 restraints weight = 12231.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.1074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071  10223  Z= 0.348
  Angle     :  0.516   8.943  13797  Z= 0.283
  Chirality :  0.040   0.357   1532
  Planarity :  0.005   0.138   1786
  Dihedral  :  9.835 128.861   1525
  Min Nonbonded Distance : 1.828

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.23 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 20.99 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.25), residues: 1245
  helix:  1.23 (0.21), residues: 647
  sheet: -1.28 (0.40), residues: 167
  loop : -1.52 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 268 
 HIS   0.011   0.001   HIS B 238 
 PHE   0.011   0.001   PHE B  50 
 TYR   0.012   0.001   TYR A 368 
 ARG   0.003   0.000   ARG C 342 

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 130
  time to evaluate  : 1.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 MET cc_start: 0.8220 (tpt) cc_final: 0.7778 (tpt)
REVERT: B  112 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8201 (t)
  outliers start: 28
  outliers final: 18
  residues processed: 151
  average time/residue: 0.4611
  time to fit residues: 99.2340
Evaluate side-chains
  144 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 1.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   94 THR
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  175 GLN
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  146 GLU
Chi-restraints excluded: chain B residue  183 MET
Chi-restraints excluded: chain C residue  210 ASP
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  380 ILE
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   76 THR
Chi-restraints excluded: chain D residue  138 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 114 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 111 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 302 GLN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.124434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.092508 restraints weight = 34985.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.097381 restraints weight = 17334.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.100484 restraints weight = 11257.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.1160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  10223  Z= 0.279
  Angle     :  0.487   8.868  13797  Z= 0.266
  Chirality :  0.039   0.355   1532
  Planarity :  0.005   0.137   1786
  Dihedral  :  8.907 117.639   1525
  Min Nonbonded Distance : 1.876

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.10 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 21.76 %
    Favored  : 76.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.25), residues: 1245
  helix:  1.30 (0.21), residues: 647
  sheet: -1.22 (0.40), residues: 167
  loop : -1.49 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 268 
 HIS   0.008   0.001   HIS B 238 
 PHE   0.020   0.001   PHE A 318 
 TYR   0.011   0.001   TYR C 230 
 ARG   0.003   0.000   ARG C 342 

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 1.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 MET cc_start: 0.8224 (tpt) cc_final: 0.7774 (tpt)
REVERT: B  112 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8193 (t)
  outliers start: 21
  outliers final: 16
  residues processed: 143
  average time/residue: 0.4540
  time to fit residues: 93.9649
Evaluate side-chains
  139 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 1.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   94 THR
Chi-restraints excluded: chain A residue  175 GLN
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  146 GLU
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain C residue  210 ASP
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  378 SER
Chi-restraints excluded: chain C residue  380 ILE
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   76 THR
Chi-restraints excluded: chain D residue  271 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 113 optimal weight:    2.9990
   chunk 106 optimal weight:    4.9990
   chunk 112 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 92 optimal weight:    0.7980
   chunk 65 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 117 optimal weight:    0.5980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 302 GLN
D  81 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.126819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.094822 restraints weight = 34831.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.099725 restraints weight = 17153.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.102965 restraints weight = 11120.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.1255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073  10223  Z= 0.172
  Angle     :  0.450   8.546  13797  Z= 0.243
  Chirality :  0.038   0.355   1532
  Planarity :  0.004   0.135   1786
  Dihedral  :  8.137  98.424   1525
  Min Nonbonded Distance : 1.889

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.02 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 21.95 %
    Favored  : 76.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.25), residues: 1245
  helix:  1.51 (0.22), residues: 647
  sheet: -1.17 (0.40), residues: 167
  loop : -1.39 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.000   TRP A 268 
 HIS   0.006   0.001   HIS B 238 
 PHE   0.023   0.001   PHE A 318 
 TYR   0.008   0.001   TYR C 230 
 ARG   0.003   0.000   ARG C 342 

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 1.497 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 MET cc_start: 0.8175 (tpt) cc_final: 0.7745 (tpt)
REVERT: A  347 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6758 (tp30)
REVERT: A  350 ARG cc_start: 0.8344 (mtt180) cc_final: 0.7709 (mtm110)
REVERT: B  112 VAL cc_start: 0.8447 (OUTLIER) cc_final: 0.8146 (t)
  outliers start: 19
  outliers final: 14
  residues processed: 144
  average time/residue: 0.4848
  time to fit residues: 102.6410
Evaluate side-chains
  141 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 1.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  175 GLN
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  347 GLU
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  146 GLU
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  378 SER
Chi-restraints excluded: chain C residue  380 ILE
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   76 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 85 optimal weight:    8.9990
   chunk 50 optimal weight:    0.1980
   chunk 7 optimal weight:    0.6980
   chunk 20 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 302 GLN
C 308 GLN
** D 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.126428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.094568 restraints weight = 34845.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.099469 restraints weight = 17210.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.102692 restraints weight = 11140.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.1329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074  10223  Z= 0.210
  Angle     :  0.457   8.533  13797  Z= 0.248
  Chirality :  0.038   0.357   1532
  Planarity :  0.004   0.135   1786
  Dihedral  :  7.605  86.371   1525
  Min Nonbonded Distance : 1.876

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.02 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 22.81 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.25), residues: 1245
  helix:  1.57 (0.21), residues: 646
  sheet: -1.17 (0.40), residues: 167
  loop : -1.43 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 268 
 HIS   0.008   0.001   HIS B 238 
 PHE   0.012   0.001   PHE A 318 
 TYR   0.009   0.001   TYR A 304 
 ARG   0.004   0.000   ARG C 342 

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 1.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 MET cc_start: 0.8144 (tpt) cc_final: 0.7721 (tpt)
REVERT: A  347 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6794 (tp30)
REVERT: A  350 ARG cc_start: 0.8323 (mtt180) cc_final: 0.7717 (mtm110)
  outliers start: 17
  outliers final: 14
  residues processed: 144
  average time/residue: 0.4771
  time to fit residues: 99.3435
Evaluate side-chains
  142 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 1.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  175 GLN
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  347 GLU
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  146 GLU
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  378 SER
Chi-restraints excluded: chain C residue  380 ILE
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   76 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 71 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 106 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 82 optimal weight:    4.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 302 GLN
C 308 GLN
** D 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.126424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.094493 restraints weight = 34949.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.099464 restraints weight = 17076.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.102713 restraints weight = 11006.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.1379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075  10223  Z= 0.195
  Angle     :  0.455   8.495  13797  Z= 0.246
  Chirality :  0.038   0.357   1532
  Planarity :  0.004   0.134   1786
  Dihedral  :  7.503  88.342   1525
  Min Nonbonded Distance : 1.886

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.86 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 22.90 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.25), residues: 1245
  helix:  1.62 (0.21), residues: 646
  sheet: -1.06 (0.40), residues: 165
  loop : -1.44 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP A 268 
 HIS   0.007   0.001   HIS B 238 
 PHE   0.030   0.001   PHE A 318 
 TYR   0.008   0.001   TYR A 304 
 ARG   0.004   0.000   ARG C 342 

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 1.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 MET cc_start: 0.7375 (ttp) cc_final: 0.7098 (mtp)
REVERT: A  318 PHE cc_start: 0.7419 (m-10) cc_final: 0.7219 (m-10)
REVERT: A  339 MET cc_start: 0.8135 (tpt) cc_final: 0.7748 (tpt)
REVERT: B  184 ARG cc_start: 0.7560 (mtm-85) cc_final: 0.7215 (mtm-85)
  outliers start: 16
  outliers final: 12
  residues processed: 141
  average time/residue: 0.4568
  time to fit residues: 92.8126
Evaluate side-chains
  140 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 128
  time to evaluate  : 1.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   94 THR
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  146 GLU
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  378 SER
Chi-restraints excluded: chain C residue  380 ILE
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   76 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 32 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 27 optimal weight:    0.0980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 302 GLN
C 261 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.128225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.096414 restraints weight = 34671.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.101415 restraints weight = 16965.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.104604 restraints weight = 10929.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.1473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077  10223  Z= 0.163
  Angle     :  0.441   8.476  13797  Z= 0.238
  Chirality :  0.038   0.355   1532
  Planarity :  0.004   0.134   1786
  Dihedral  :  7.313  88.626   1525
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.22 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 23.00 %
    Favored  : 75.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.25), residues: 1245
  helix:  1.70 (0.22), residues: 648
  sheet: -1.00 (0.40), residues: 165
  loop : -1.42 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP A 268 
 HIS   0.006   0.001   HIS B 238 
 PHE   0.018   0.001   PHE A 318 
 TYR   0.018   0.001   TYR C 230 
 ARG   0.004   0.000   ARG C 342 

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 1.494 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 MET cc_start: 0.7349 (ttp) cc_final: 0.7066 (mtp)
REVERT: A  339 MET cc_start: 0.8076 (tpt) cc_final: 0.7753 (tpt)
REVERT: A  350 ARG cc_start: 0.8281 (mtt180) cc_final: 0.7620 (mtm110)
REVERT: B  184 ARG cc_start: 0.7475 (mtm-85) cc_final: 0.7135 (mtm-85)
REVERT: C  273 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7687 (tp40)
  outliers start: 14
  outliers final: 11
  residues processed: 144
  average time/residue: 0.4572
  time to fit residues: 94.4621
Evaluate side-chains
  137 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 126
  time to evaluate  : 1.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  175 GLN
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  146 GLU
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  378 SER
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   76 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   chunk 86 optimal weight:    4.9990
   chunk 108 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 7 optimal weight:    0.1980
   chunk 67 optimal weight:    1.9990
   chunk 61 optimal weight:    9.9990
   chunk 23 optimal weight:   10.0000
   chunk 83 optimal weight:    3.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
A 302 GLN
** D 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.126511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.094791 restraints weight = 34915.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.099735 restraints weight = 17126.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.102937 restraints weight = 11031.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.1509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078  10223  Z= 0.215
  Angle     :  0.458   8.624  13797  Z= 0.248
  Chirality :  0.038   0.359   1532
  Planarity :  0.004   0.134   1786
  Dihedral  :  7.339  88.272   1524
  Min Nonbonded Distance : 1.893

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.94 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 23.19 %
    Favored  : 75.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.25), residues: 1245
  helix:  1.64 (0.21), residues: 651
  sheet: -1.03 (0.40), residues: 165
  loop : -1.40 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 268 
 HIS   0.008   0.001   HIS B 238 
 PHE   0.019   0.001   PHE A 318 
 TYR   0.015   0.001   TYR C 230 
 ARG   0.003   0.000   ARG C 342 

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 131
  time to evaluate  : 1.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 MET cc_start: 0.7350 (ttp) cc_final: 0.7067 (mtp)
REVERT: A  350 ARG cc_start: 0.8312 (mtt180) cc_final: 0.7624 (mtm110)
REVERT: C  235 GLU cc_start: 0.7972 (tt0) cc_final: 0.7530 (tp30)
  outliers start: 11
  outliers final: 11
  residues processed: 141
  average time/residue: 0.4661
  time to fit residues: 94.1081
Evaluate side-chains
  141 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 130
  time to evaluate  : 1.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  175 GLN
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain B residue   53 ASP
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  146 GLU
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   76 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 102 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 98 optimal weight:    0.2980
   chunk 51 optimal weight:    1.9990
   chunk 119 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 36 optimal weight:    0.3980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** D 238 HIS ** 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 = 0.3311 r_free = 0.3311 target = 0.126730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.094632 restraints weight = 35144.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.099586 restraints weight = 17278.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.102722 restraints weight = 11209.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.1541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077  10223  Z= 0.225
  Angle     :  0.465   8.709  13797  Z= 0.252
  Chirality :  0.039   0.359   1532
  Planarity :  0.004   0.135   1786
  Dihedral  :  7.332  86.604   1524
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.70 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 22.81 %
    Favored  : 75.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.25), residues: 1245
  helix:  1.64 (0.21), residues: 649
  sheet: -1.02 (0.40), residues: 165
  loop : -1.41 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 268 
 HIS   0.007   0.001   HIS B 238 
 PHE   0.031   0.001   PHE A 318 
 TYR   0.014   0.001   TYR C 230 
 ARG   0.003   0.000   ARG C 342 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5333.22 seconds
wall clock time: 95 minutes 30.95 seconds (5730.95 seconds total)