Starting phenix.real_space_refine
on Tue Jun 17 05:19:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v24_42897/06_2025/8v24_42897_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v24_42897/06_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_42897/06_2025/8v24_42897.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v24_42897/06_2025/8v24_42897.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v24_42897/06_2025/8v24_42897_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v24_42897/06_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-5710/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: 9.76, per 1000 atoms: 0.50
  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: 5.39
  Conformation dependent library (CDL) restraints added in 1.5 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: 1.68
  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: 6.88

  Time building geometry restraints manager: 6.40 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:                  0.000
  Normalize map: mean=0, sd=1:             0.510
  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:             0.360
  Extract box with map and model:          0.790
  Check model and map are aligned:         0.150
  Set scattering table:                    0.190
  Process input model:                     49.910
  Find NCS groups from input model:        0.640
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   55.420
-------------------------------------------------------------------------------
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  10235  Z= 0.209
  Angle     :  0.633  11.426  13809  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13179 (  515)
  hydrogen bonds       : angle       5.27168 ( 1539)
  metal coordination   : bond        0.00537 (   12)
  metal coordination   : angle       2.26449 (   12)
  covalent geometry    : bond        0.00414 (10223)
  covalent geometry    : angle       0.63019 (13797)

*********************** 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  : 1.495 
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: 0.4680
  time to fit residues: 92.0606
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  : 1.386 
-------------------------------------------------------------------------------
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 = 43)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.092498 restraints weight = 35145.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.097281 restraints weight = 17452.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.100350 restraints weight = 11358.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
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  10235  Z= 0.199
  Angle     :  0.565   9.168  13809  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03977 (  515)
  hydrogen bonds       : angle       4.27374 ( 1539)
  metal coordination   : bond        0.00938 (   12)
  metal coordination   : angle       2.72531 (   12)
  covalent geometry    : bond        0.00464 (10223)
  covalent geometry    : angle       0.55974 (13797)

*********************** 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  : 1.560 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7614 (mp)
REVERT: B  112 VAL cc_start: 0.8463 (OUTLIER) cc_final: 0.8160 (t)
REVERT: B  200 TYR cc_start: 0.8687 (t80) cc_final: 0.8000 (t80)
REVERT: D    9 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7831 (mtm110)
  outliers start: 17
  outliers final: 9
  residues processed: 152
  average time/residue: 0.4661
  time to fit residues: 101.3953
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  : 1.633 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 5 optimal weight:    0.9990
   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:    1.0386

-------------------------------------------------------------------------------
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 = 0.3299 r_free = 0.3299 target = 0.126107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.094496 restraints weight = 34729.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.099407 restraints weight = 17110.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.102583 restraints weight = 11065.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.0883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074  10235  Z= 0.121
  Angle     :  0.471   8.713  13809  Z= 0.250
  Chirality :  0.038   0.354   1532
  Planarity :  0.005   0.138   1786
  Dihedral  : 10.149 123.566   1525
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.30 %
    Favored  : 94.54 %
  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 : 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:  0.17 (0.25), residues: 1245
  helix:  1.43 (0.22), residues: 646
  sheet: -1.23 (0.40), residues: 167
  loop : -1.32 (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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03320 (  515)
  hydrogen bonds       : angle       3.93789 ( 1539)
  metal coordination   : bond        0.00551 (   12)
  metal coordination   : angle       2.22857 (   12)
  covalent geometry    : bond        0.00283 (10223)
  covalent geometry    : angle       0.46658 (13797)

*********************** 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  : 1.611 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7629 (mp)
REVERT: A  339 MET cc_start: 0.8185 (tpt) cc_final: 0.7733 (tpt)
REVERT: B  112 VAL cc_start: 0.8436 (OUTLIER) cc_final: 0.8128 (t)
REVERT: B  292 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7301 (mt-10)
  outliers start: 21
  outliers final: 13
  residues processed: 154
  average time/residue: 0.4794
  time to fit residues: 107.6419
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  : 1.400 
-------------------------------------------------------------------------------
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:    5.9990
   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:    1.9990
   chunk 111 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 39 optimal weight:    0.5980
   overall best weight:    1.7188

-------------------------------------------------------------------------------
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 = 0.3278 r_free = 0.3278 target = 0.124334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.093392 restraints weight = 35168.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.097972 restraints weight = 18154.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.100866 restraints weight = 12060.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.1050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071  10235  Z= 0.181
  Angle     :  0.494   8.783  13809  Z= 0.266
  Chirality :  0.039   0.356   1532
  Planarity :  0.005   0.137   1786
  Dihedral  :  9.803 129.723   1525
  Min Nonbonded Distance : 1.841

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.91 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 21.18 %
    Favored  : 76.53 %
  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:  0.02 (0.25), residues: 1245
  helix:  1.33 (0.21), residues: 647
  sheet: -1.25 (0.40), residues: 167
  loop : -1.46 (0.30), residues: 431

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   0.010   0.001   PHE B  50 
 TYR   0.010   0.001   TYR A 368 
 ARG   0.003   0.000   ARG C 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03371 (  515)
  hydrogen bonds       : angle       3.91478 ( 1539)
  metal coordination   : bond        0.00869 (   12)
  metal coordination   : angle       2.65299 (   12)
  covalent geometry    : bond        0.00429 (10223)
  covalent geometry    : angle       0.48844 (13797)

*********************** 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
  156 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 1.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 MET cc_start: 0.8200 (tpt) cc_final: 0.7761 (tpt)
REVERT: C  315 MET cc_start: 0.8330 (mmp) cc_final: 0.8120 (mmt)
  outliers start: 24
  outliers final: 17
  residues processed: 150
  average time/residue: 0.4610
  time to fit residues: 99.1910
Evaluate side-chains
  141 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 1.494 
-------------------------------------------------------------------------------
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  146 GLU
Chi-restraints excluded: chain B residue  147 PHE
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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 114 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 111 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    1.7990

-------------------------------------------------------------------------------
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 = 0.3281 r_free = 0.3281 target = 0.124533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.092569 restraints weight = 35041.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.097426 restraints weight = 17340.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.100564 restraints weight = 11275.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.1140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  10235  Z= 0.182
  Angle     :  0.493   8.758  13809  Z= 0.265
  Chirality :  0.039   0.355   1532
  Planarity :  0.005   0.136   1786
  Dihedral  :  8.937 116.886   1525
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.35 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 21.47 %
    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:  0.04 (0.25), residues: 1245
  helix:  1.35 (0.21), residues: 647
  sheet: -1.21 (0.40), residues: 167
  loop : -1.48 (0.30), 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   0.019   0.001   PHE A 318 
 TYR   0.011   0.001   TYR C 230 
 ARG   0.003   0.000   ARG C 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03294 (  515)
  hydrogen bonds       : angle       3.87788 ( 1539)
  metal coordination   : bond        0.00888 (   12)
  metal coordination   : angle       2.69564 (   12)
  covalent geometry    : bond        0.00430 (10223)
  covalent geometry    : angle       0.48668 (13797)

*********************** 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
  150 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 1.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  318 PHE cc_start: 0.8239 (m-80) cc_final: 0.7940 (m-10)
REVERT: A  339 MET cc_start: 0.8222 (tpt) cc_final: 0.7777 (tpt)
REVERT: A  348 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.7873 (ptmm)
REVERT: B  112 VAL cc_start: 0.8485 (OUTLIER) cc_final: 0.8183 (t)
  outliers start: 23
  outliers final: 14
  residues processed: 147
  average time/residue: 0.4745
  time to fit residues: 101.1063
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  : 1.521 
-------------------------------------------------------------------------------
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  348 LYS
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 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  138 VAL
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:    0.6980
   chunk 70 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 117 optimal weight:    0.8980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
D  81 ASN
** 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 = 0.3298 r_free = 0.3298 target = 0.125963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.094021 restraints weight = 34806.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.098958 restraints weight = 17046.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.102167 restraints weight = 11008.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.1251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074  10235  Z= 0.125
  Angle     :  0.457   8.630  13809  Z= 0.244
  Chirality :  0.038   0.356   1532
  Planarity :  0.004   0.135   1786
  Dihedral  :  8.058  92.380   1525
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.18 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 21.85 %
    Favored  : 76.43 %
  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:  0.23 (0.25), residues: 1245
  helix:  1.54 (0.21), residues: 646
  sheet: -1.18 (0.40), residues: 167
  loop : -1.42 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 268 
 HIS   0.007   0.001   HIS B 238 
 PHE   0.007   0.001   PHE D 258 
 TYR   0.008   0.001   TYR C 230 
 ARG   0.003   0.000   ARG C 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02996 (  515)
  hydrogen bonds       : angle       3.73189 ( 1539)
  metal coordination   : bond        0.00594 (   12)
  metal coordination   : angle       2.17420 (   12)
  covalent geometry    : bond        0.00296 (10223)
  covalent geometry    : angle       0.45226 (13797)

*********************** 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
  150 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 1.702 
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: 0.8185 (tpt) cc_final: 0.7761 (tpt)
REVERT: B  112 VAL cc_start: 0.8445 (OUTLIER) cc_final: 0.8142 (t)
  outliers start: 18
  outliers final: 13
  residues processed: 147
  average time/residue: 0.4394
  time to fit residues: 93.9704
Evaluate side-chains
  138 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 124
  time to evaluate  : 1.414 
-------------------------------------------------------------------------------
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   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 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:    1.9990
   chunk 85 optimal weight:    8.9990
   chunk 50 optimal weight:    2.9990
   chunk 7 optimal weight:    0.1980
   chunk 20 optimal weight:    4.9990
   chunk 86 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    2.0388

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

Flipped N/Q/H residues before XYZ refinement:
C 308 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 = 0.3280 r_free = 0.3280 target = 0.124393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.092715 restraints weight = 35112.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.097450 restraints weight = 17534.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.100542 restraints weight = 11472.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.1287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073  10235  Z= 0.205
  Angle     :  0.506   8.845  13809  Z= 0.273
  Chirality :  0.040   0.358   1532
  Planarity :  0.005   0.136   1786
  Dihedral  :  7.748  87.869   1525
  Min Nonbonded Distance : 1.846

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.59 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 22.52 %
    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:  0.07 (0.25), residues: 1245
  helix:  1.43 (0.21), residues: 646
  sheet: -1.17 (0.40), residues: 165
  loop : -1.56 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 268 
 HIS   0.010   0.001   HIS B 238 
 PHE   0.010   0.001   PHE B  50 
 TYR   0.012   0.001   TYR A 368 
 ARG   0.003   0.000   ARG C 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03327 (  515)
  hydrogen bonds       : angle       3.85072 ( 1539)
  metal coordination   : bond        0.00983 (   12)
  metal coordination   : angle       2.83713 (   12)
  covalent geometry    : bond        0.00486 (10223)
  covalent geometry    : angle       0.49966 (13797)

*********************** 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
  150 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 1.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 MET cc_start: 0.7404 (ttp) cc_final: 0.7160 (mtp)
REVERT: A  339 MET cc_start: 0.8266 (tpt) cc_final: 0.7826 (tpt)
REVERT: B  112 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.8203 (t)
REVERT: D  100 GLU cc_start: 0.8263 (tt0) cc_final: 0.8046 (tt0)
  outliers start: 19
  outliers final: 15
  residues processed: 148
  average time/residue: 0.4585
  time to fit residues: 98.3021
Evaluate side-chains
  145 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 1.553 
-------------------------------------------------------------------------------
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   90 ASP
Chi-restraints excluded: chain B residue  112 VAL
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
Chi-restraints excluded: chain D residue  271 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 76 optimal weight:    7.9990
   chunk 71 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 106 optimal weight:    0.0370
   chunk 77 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 82 optimal weight:    4.9990
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.9062

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

Flipped N/Q/H residues before XYZ refinement:
C 308 GLN

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 = 0.126453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.094598 restraints weight = 34955.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.099528 restraints weight = 17018.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.102767 restraints weight = 10973.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.1370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075  10235  Z= 0.112
  Angle     :  0.452   8.609  13809  Z= 0.242
  Chirality :  0.038   0.356   1532
  Planarity :  0.004   0.135   1786
  Dihedral  :  7.506  89.206   1525
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.14 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 22.52 %
    Favored  : 76.05 %
  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:  0.30 (0.25), residues: 1245
  helix:  1.63 (0.22), residues: 646
  sheet: -1.07 (0.40), residues: 165
  loop : -1.46 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP A 268 
 HIS   0.005   0.001   HIS B 238 
 PHE   0.014   0.001   PHE A 318 
 TYR   0.008   0.001   TYR A 304 
 ARG   0.004   0.000   ARG C 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02913 (  515)
  hydrogen bonds       : angle       3.64170 ( 1539)
  metal coordination   : bond        0.00525 (   12)
  metal coordination   : angle       2.14616 (   12)
  covalent geometry    : bond        0.00266 (10223)
  covalent geometry    : angle       0.44793 (13797)

*********************** 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
  142 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 1.397 
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: 0.7371 (ttp) cc_final: 0.7114 (mtp)
REVERT: A  339 MET cc_start: 0.8177 (tpt) cc_final: 0.7772 (tpt)
REVERT: B  112 VAL cc_start: 0.8443 (OUTLIER) cc_final: 0.8142 (t)
REVERT: B  184 ARG cc_start: 0.7490 (mtm-85) cc_final: 0.7144 (mtm-85)
  outliers start: 15
  outliers final: 14
  residues processed: 140
  average time/residue: 0.4391
  time to fit residues: 88.6033
Evaluate side-chains
  139 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 124
  time to evaluate  : 1.386 
-------------------------------------------------------------------------------
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   90 ASP
Chi-restraints excluded: chain B residue  112 VAL
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:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
C 261 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 = 0.3287 r_free = 0.3287 target = 0.125042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.093189 restraints weight = 34862.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.098044 restraints weight = 17205.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.101222 restraints weight = 11182.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.1401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076  10235  Z= 0.167
  Angle     :  0.481   8.820  13809  Z= 0.259
  Chirality :  0.039   0.360   1532
  Planarity :  0.004   0.135   1786
  Dihedral  :  7.524  85.301   1525
  Min Nonbonded Distance : 1.871

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.10 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 22.71 %
    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:  0.22 (0.25), residues: 1245
  helix:  1.52 (0.21), residues: 649
  sheet: -1.10 (0.40), residues: 165
  loop : -1.48 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 268 
 HIS   0.009   0.001   HIS B 238 
 PHE   0.021   0.001   PHE A 318 
 TYR   0.019   0.001   TYR C 230 
 ARG   0.004   0.000   ARG C 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03104 (  515)
  hydrogen bonds       : angle       3.70207 ( 1539)
  metal coordination   : bond        0.00793 (   12)
  metal coordination   : angle       2.50265 (   12)
  covalent geometry    : bond        0.00399 (10223)
  covalent geometry    : angle       0.47568 (13797)

*********************** 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
  143 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 1.433 
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: 0.7377 (ttp) cc_final: 0.7121 (mtp)
REVERT: A  339 MET cc_start: 0.8165 (tpt) cc_final: 0.7783 (tpt)
REVERT: B  112 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8171 (t)
  outliers start: 17
  outliers final: 16
  residues processed: 141
  average time/residue: 0.4358
  time to fit residues: 88.9627
Evaluate side-chains
  143 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 1.415 
-------------------------------------------------------------------------------
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   53 ASP
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 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9980
   chunk 86 optimal weight:    3.9990
   chunk 108 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 23 optimal weight:   10.0000
   chunk 83 optimal weight:    0.7980
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.3297 r_free = 0.3297 target = 0.125979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.095093 restraints weight = 34796.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.099701 restraints weight = 17851.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.102671 restraints weight = 11776.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.1446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077  10235  Z= 0.125
  Angle     :  0.457   8.758  13809  Z= 0.245
  Chirality :  0.038   0.358   1532
  Planarity :  0.004   0.135   1786
  Dihedral  :  7.408  85.923   1525
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.06 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 22.61 %
    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:  0.33 (0.25), residues: 1245
  helix:  1.61 (0.21), residues: 649
  sheet: -1.02 (0.41), residues: 165
  loop : -1.43 (0.30), residues: 431

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   0.021   0.001   PHE A 318 
 TYR   0.016   0.001   TYR C 230 
 ARG   0.004   0.000   ARG C 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02906 (  515)
  hydrogen bonds       : angle       3.60696 ( 1539)
  metal coordination   : bond        0.00589 (   12)
  metal coordination   : angle       2.17010 (   12)
  covalent geometry    : bond        0.00298 (10223)
  covalent geometry    : angle       0.45288 (13797)

********************** 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
  147 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 1.564 
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: 0.7379 (ttp) cc_final: 0.7125 (mtp)
REVERT: A  339 MET cc_start: 0.8135 (tpt) cc_final: 0.7770 (tpt)
REVERT: B  112 VAL cc_start: 0.8484 (OUTLIER) cc_final: 0.8183 (t)
  outliers start: 16
  outliers final: 15
  residues processed: 145
  average time/residue: 0.4533
  time to fit residues: 95.6898
Evaluate side-chains
  145 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 1.634 
-------------------------------------------------------------------------------
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   53 ASP
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 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 102 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 87 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 119 optimal weight:    0.8980
   chunk 78 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 = 0.3319 r_free = 0.3319 target = 0.127369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.095423 restraints weight = 35097.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.100305 restraints weight = 17244.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.103495 restraints weight = 11152.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.1542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078  10235  Z= 0.118
  Angle     :  0.453   8.715  13809  Z= 0.243
  Chirality :  0.038   0.361   1532
  Planarity :  0.004   0.135   1786
  Dihedral  :  7.330  85.842   1525
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.62 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 22.42 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.39 (0.25), residues: 1245
  helix:  1.67 (0.21), residues: 649
  sheet: -0.99 (0.41), residues: 165
  loop : -1.42 (0.30), residues: 431

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   0.017   0.001   PHE A 318 
 TYR   0.013   0.001   TYR C 230 
 ARG   0.007   0.000   ARG B 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02861 (  515)
  hydrogen bonds       : angle       3.57602 ( 1539)
  metal coordination   : bond        0.00545 (   12)
  metal coordination   : angle       2.13588 (   12)
  covalent geometry    : bond        0.00283 (10223)
  covalent geometry    : angle       0.44899 (13797)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5613.85 seconds
wall clock time: 96 minutes 55.49 seconds (5815.49 seconds total)