Starting phenix.real_space_refine
on Sun Aug 24 11:36:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v24_42897/08_2025/8v24_42897_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v24_42897/08_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_42897/08_2025/8v24_42897.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v24_42897/08_2025/8v24_42897.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v24_42897/08_2025/8v24_42897_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v24_42897/08_2025/8v24_42897_trim.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.98, per 1000 atoms: 0.15
  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: 1.56
  Conformation dependent library (CDL) restraints added in 534.5 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  
  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: 0.55
  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: 4.49

  Time building geometry restraints manager: 2.24 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 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:             0.490
  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:             0.120
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     21.640
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.700
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG A 333 
 TYR   0.011   0.001   TYR C 230 
 PHE   0.042   0.001   PHE D  50 
 TRP   0.006   0.001   TRP A 268 
 HIS   0.006   0.001   HIS B 238 

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

*********************** 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  : 0.466 
Fit side-chains
   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: 0.7568 (mtt)
  outliers start: 5
  outliers final: 2
  residues processed: 139
  average time/residue: 0.2388
  time to fit residues: 46.7284
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  : 0.596 
-------------------------------------------------------------------------------
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 108 optimal weight:    0.8980
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    0.4980
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 123 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.3297 r_free = 0.3297 target = 0.126084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.095311 restraints weight = 34995.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.099822 restraints weight = 18268.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.102707 restraints weight = 12181.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.104738 restraints weight = 9343.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.105909 restraints weight = 7832.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.0668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10235  Z= 0.128
  Angle     :  0.521   8.896  13809  Z= 0.268
  Chirality :  0.039   0.351   1532
  Planarity :  0.005   0.142   1786
  Dihedral  : 14.234 175.707   1526
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.78 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 20.61 %
    Favored  : 77.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.14 (0.25), residues: 1245
  helix:  1.39 (0.22), residues: 643
  sheet: -1.42 (0.40), residues: 162
  loop : -1.20 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  80 
 TYR   0.008   0.001   TYR C 230 
 PHE   0.009   0.001   PHE D  50 
 TRP   0.005   0.000   TRP A 268 
 HIS   0.007   0.001   HIS B 238 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (10223)
  covalent geometry    : angle       0.51697 (13797)
  hydrogen bonds       : bond        0.03675 (  515)
  hydrogen bonds       : angle       4.13686 ( 1539)
  metal coordination   : bond        0.00551 (   12)
  metal coordination   : angle       2.17611 (   12)

*********************** 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
  161 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 144
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7655 (mp)
REVERT: B  112 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8085 (t)
  outliers start: 17
  outliers final: 9
  residues processed: 154
  average time/residue: 0.2003
  time to fit residues: 44.6346
Evaluate side-chains
  142 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 131
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ILE
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  147 PHE
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  175 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 111 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 108 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 90 optimal weight:    3.9990
   overall best weight:    1.7386

-------------------------------------------------------------------------------
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 = 0.3275 r_free = 0.3275 target = 0.124335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.092472 restraints weight = 35097.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.097309 restraints weight = 17410.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.100401 restraints weight = 11320.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.102442 restraints weight = 8594.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.103764 restraints weight = 7167.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.0866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074  10235  Z= 0.184
  Angle     :  0.507   8.918  13809  Z= 0.271
  Chirality :  0.039   0.356   1532
  Planarity :  0.005   0.139   1786
  Dihedral  : 10.420 128.618   1525
  Min Nonbonded Distance : 1.833

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.51 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 20.80 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.00 (0.25), residues: 1245
  helix:  1.30 (0.21), residues: 646
  sheet: -1.31 (0.40), residues: 167
  loop : -1.43 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  80 
 TYR   0.009   0.001   TYR C 230 
 PHE   0.009   0.001   PHE B  50 
 TRP   0.005   0.001   TRP A 268 
 HIS   0.010   0.001   HIS B 238 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 (10223)
  covalent geometry    : angle       0.50085 (13797)
  hydrogen bonds       : bond        0.03583 (  515)
  hydrogen bonds       : angle       4.01590 ( 1539)
  metal coordination   : bond        0.00890 (   12)
  metal coordination   : angle       2.72245 (   12)

*********************** 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
  165 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 142
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7749 (mp)
REVERT: A  339 MET cc_start: 0.8179 (tpt) cc_final: 0.7818 (tpt)
  outliers start: 23
  outliers final: 15
  residues processed: 159
  average time/residue: 0.2215
  time to fit residues: 49.5330
Evaluate side-chains
  148 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
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  146 GLU
Chi-restraints excluded: chain B residue  183 MET
Chi-restraints excluded: chain C residue  210 ASP
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  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
Chi-restraints excluded: chain D residue   90 ASP
Chi-restraints excluded: chain D residue  175 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 42 optimal weight:    0.7980
   chunk 85 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 56 optimal weight:    1.9990
   chunk 108 optimal weight:    1.9990
   chunk 119 optimal weight:    0.9980
   chunk 103 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3297 r_free = 0.3297 target = 0.126172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.094283 restraints weight = 34899.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.099205 restraints weight = 17155.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.102306 restraints weight = 11115.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.104393 restraints weight = 8400.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.105588 restraints weight = 7004.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.1076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072  10235  Z= 0.123
  Angle     :  0.460   8.766  13809  Z= 0.245
  Chirality :  0.038   0.354   1532
  Planarity :  0.004   0.137   1786
  Dihedral  :  9.796 128.017   1525
  Min Nonbonded Distance : 1.891

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.30 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 22.04 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.16 (0.25), residues: 1245
  helix:  1.45 (0.22), residues: 646
  sheet: -1.24 (0.40), residues: 167
  loop : -1.38 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 342 
 TYR   0.007   0.001   TYR C 230 
 PHE   0.008   0.001   PHE C 318 
 TRP   0.005   0.001   TRP A 268 
 HIS   0.006   0.001   HIS B 238 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (10223)
  covalent geometry    : angle       0.45497 (13797)
  hydrogen bonds       : bond        0.03104 (  515)
  hydrogen bonds       : angle       3.81423 ( 1539)
  metal coordination   : bond        0.00559 (   12)
  metal coordination   : angle       2.24795 (   12)

*********************** 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
  148 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 135
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 MET cc_start: 0.8160 (tpt) cc_final: 0.7819 (tpt)
REVERT: B  112 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8089 (t)
  outliers start: 13
  outliers final: 10
  residues processed: 144
  average time/residue: 0.2228
  time to fit residues: 45.7640
Evaluate side-chains
  137 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 126
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ILE
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   76 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 98 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 119 optimal weight:    3.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
C 261 GLN
C 308 GLN
** D 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.125887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.094978 restraints weight = 34867.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.099669 restraints weight = 17864.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.102668 restraints weight = 11766.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.104371 restraints weight = 8980.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.105891 restraints weight = 7596.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.1190

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= 0.131
  Angle     :  0.459   8.528  13809  Z= 0.246
  Chirality :  0.038   0.353   1532
  Planarity :  0.004   0.135   1786
  Dihedral  :  8.999 115.026   1525
  Min Nonbonded Distance : 1.881

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.94 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 22.04 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.25), residues: 1245
  helix:  1.52 (0.21), residues: 647
  sheet: -1.21 (0.40), residues: 167
  loop : -1.39 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 342 
 TYR   0.015   0.001   TYR C 230 
 PHE   0.007   0.001   PHE B  50 
 TRP   0.005   0.000   TRP A 268 
 HIS   0.008   0.001   HIS B 238 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (10223)
  covalent geometry    : angle       0.45413 (13797)
  hydrogen bonds       : bond        0.03050 (  515)
  hydrogen bonds       : angle       3.75168 ( 1539)
  metal coordination   : bond        0.00619 (   12)
  metal coordination   : angle       2.26046 (   12)

*********************** 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
  148 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 MET cc_start: 0.7356 (ttp) cc_final: 0.7067 (mtp)
REVERT: A  339 MET cc_start: 0.8172 (tpt) cc_final: 0.7808 (tpt)
REVERT: B  112 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8099 (t)
REVERT: B  184 ARG cc_start: 0.7569 (mtm-85) cc_final: 0.7208 (mtm-85)
  outliers start: 19
  outliers final: 14
  residues processed: 145
  average time/residue: 0.2263
  time to fit residues: 47.4904
Evaluate side-chains
  141 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  175 GLN
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 75 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 122 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 119 optimal weight:    2.9990
   chunk 112 optimal weight:    2.9990
   chunk 76 optimal weight:    6.9990
   chunk 96 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3288 r_free = 0.3288 target = 0.125303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.093523 restraints weight = 34762.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.098389 restraints weight = 17152.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.101537 restraints weight = 11131.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.103629 restraints weight = 8390.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.104847 restraints weight = 6976.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.1225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074  10235  Z= 0.164
  Angle     :  0.480   8.642  13809  Z= 0.257
  Chirality :  0.039   0.356   1532
  Planarity :  0.004   0.135   1786
  Dihedral  :  8.025  85.481   1525
  Min Nonbonded Distance : 1.872

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.27 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 21.47 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.20 (0.25), residues: 1245
  helix:  1.53 (0.21), residues: 646
  sheet: -1.22 (0.40), residues: 167
  loop : -1.44 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 342 
 TYR   0.014   0.001   TYR C 230 
 PHE   0.030   0.001   PHE A 318 
 TRP   0.004   0.001   TRP A 268 
 HIS   0.008   0.001   HIS B 238 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 (10223)
  covalent geometry    : angle       0.47408 (13797)
  hydrogen bonds       : bond        0.03145 (  515)
  hydrogen bonds       : angle       3.73398 ( 1539)
  metal coordination   : bond        0.00787 (   12)
  metal coordination   : angle       2.50995 (   12)

*********************** 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
  149 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 0.593 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 MET cc_start: 0.8127 (tpt) cc_final: 0.7756 (tpt)
REVERT: B  112 VAL cc_start: 0.8421 (OUTLIER) cc_final: 0.8124 (t)
  outliers start: 22
  outliers final: 14
  residues processed: 145
  average time/residue: 0.2296
  time to fit residues: 47.7056
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  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  175 GLN
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  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 1 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 106 optimal weight:    4.9990
   chunk 75 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 108 optimal weight:    0.4980
   chunk 77 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 118 optimal weight:    0.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    1.0786

-------------------------------------------------------------------------------
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 = 0.3303 r_free = 0.3303 target = 0.126557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.094649 restraints weight = 34980.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.099595 restraints weight = 17170.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.102823 restraints weight = 11094.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.104831 restraints weight = 8355.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.106108 restraints weight = 6945.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.1305

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= 0.123
  Angle     :  0.457   8.534  13809  Z= 0.245
  Chirality :  0.038   0.356   1532
  Planarity :  0.004   0.135   1786
  Dihedral  :  7.464  85.939   1525
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.46 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 22.14 %
    Favored  : 76.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.25), residues: 1245
  helix:  1.59 (0.21), residues: 649
  sheet: -1.18 (0.40), residues: 167
  loop : -1.37 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 342 
 TYR   0.017   0.001   TYR C 230 
 PHE   0.019   0.001   PHE A 318 
 TRP   0.005   0.000   TRP A 268 
 HIS   0.006   0.001   HIS B 238 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (10223)
  covalent geometry    : angle       0.45256 (13797)
  hydrogen bonds       : bond        0.02955 (  515)
  hydrogen bonds       : angle       3.64922 ( 1539)
  metal coordination   : bond        0.00586 (   12)
  metal coordination   : angle       2.22739 (   12)

*********************** 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
  144 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 0.633 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 MET cc_start: 0.8100 (tpt) cc_final: 0.7754 (tpt)
REVERT: B  112 VAL cc_start: 0.8382 (OUTLIER) cc_final: 0.8084 (t)
REVERT: B  184 ARG cc_start: 0.7559 (mtm-85) cc_final: 0.7209 (mtm-85)
  outliers start: 17
  outliers final: 14
  residues processed: 141
  average time/residue: 0.2252
  time to fit residues: 45.6871
Evaluate side-chains
  141 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  175 GLN
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 41 optimal weight:    0.0770
   chunk 3 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 66 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 102 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 25 optimal weight:    4.9990
   chunk 23 optimal weight:    8.9990
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.128627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.096819 restraints weight = 34685.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.101827 restraints weight = 16957.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.105029 restraints weight = 10914.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.107209 restraints weight = 8215.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.108424 restraints weight = 6795.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.1449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.077  10235  Z= 0.095
  Angle     :  0.439   8.353  13809  Z= 0.234
  Chirality :  0.038   0.360   1532
  Planarity :  0.004   0.133   1786
  Dihedral  :  7.244  85.711   1525
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.14 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 22.42 %
    Favored  : 76.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.25), residues: 1245
  helix:  1.71 (0.22), residues: 651
  sheet: -1.04 (0.40), residues: 165
  loop : -1.34 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 342 
 TYR   0.019   0.001   TYR C 230 
 PHE   0.025   0.001   PHE A 318 
 TRP   0.005   0.000   TRP A 268 
 HIS   0.006   0.001   HIS B 238 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (10223)
  covalent geometry    : angle       0.43516 (13797)
  hydrogen bonds       : bond        0.02766 (  515)
  hydrogen bonds       : angle       3.53936 ( 1539)
  metal coordination   : bond        0.00402 (   12)
  metal coordination   : angle       2.02284 (   12)

*********************** 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
  143 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 132
  time to evaluate  : 0.562 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 MET cc_start: 0.7286 (ttp) cc_final: 0.6947 (mtp)
REVERT: A  339 MET cc_start: 0.7997 (tpt) cc_final: 0.7686 (tpt)
REVERT: A  350 ARG cc_start: 0.8293 (mtt180) cc_final: 0.7811 (ptp-110)
REVERT: B  184 ARG cc_start: 0.7492 (mtm-85) cc_final: 0.7154 (mtm-85)
  outliers start: 11
  outliers final: 10
  residues processed: 141
  average time/residue: 0.2275
  time to fit residues: 46.1823
Evaluate side-chains
  134 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 124
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  146 GLU
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  378 SER
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   76 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 22 optimal weight:    5.9990
   chunk 95 optimal weight:    2.9990
   chunk 97 optimal weight:    0.7980
   chunk 76 optimal weight:    7.9990
   chunk 83 optimal weight:    3.9990
   chunk 69 optimal weight:    4.9990
   chunk 101 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 85 optimal weight:    7.9990
   chunk 91 optimal weight:    3.9990
   overall best weight:    1.6986

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.124892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.093280 restraints weight = 34930.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.098082 restraints weight = 17302.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.101164 restraints weight = 11230.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.103175 restraints weight = 8517.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.104315 restraints weight = 7115.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.1424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077  10235  Z= 0.179
  Angle     :  0.490   8.702  13809  Z= 0.264
  Chirality :  0.039   0.368   1532
  Planarity :  0.004   0.135   1786
  Dihedral  :  7.426  86.693   1524
  Min Nonbonded Distance : 1.875

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.35 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 22.61 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.27 (0.25), residues: 1245
  helix:  1.56 (0.21), residues: 651
  sheet: -1.10 (0.40), residues: 166
  loop : -1.44 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 342 
 TYR   0.011   0.001   TYR A 368 
 PHE   0.021   0.001   PHE A 318 
 TRP   0.004   0.001   TRP D 144 
 HIS   0.009   0.001   HIS B 238 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (10223)
  covalent geometry    : angle       0.48347 (13797)
  hydrogen bonds       : bond        0.03118 (  515)
  hydrogen bonds       : angle       3.68049 ( 1539)
  metal coordination   : bond        0.00839 (   12)
  metal coordination   : angle       2.65535 (   12)

*********************** 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: 14
    poor density    : 129
  time to evaluate  : 0.560 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  350 ARG cc_start: 0.8317 (mtt180) cc_final: 0.7842 (ptp-110)
  outliers start: 14
  outliers final: 13
  residues processed: 141
  average time/residue: 0.2272
  time to fit residues: 46.1609
Evaluate side-chains
  140 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 127
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  175 GLN
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  146 GLU
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  378 SER
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 56 optimal weight:    0.4980
   chunk 14 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 70 optimal weight:    0.2980
   chunk 115 optimal weight:    1.9990
   chunk 76 optimal weight:    6.9990
   chunk 64 optimal weight:    2.9990
   chunk 100 optimal weight:    1.9990
   chunk 97 optimal weight:    0.2980
   chunk 116 optimal weight:    0.7980
   chunk 88 optimal weight:   10.0000
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.128133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.096531 restraints weight = 35043.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.101513 restraints weight = 17161.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.104728 restraints weight = 11067.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.106811 restraints weight = 8294.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.108196 restraints weight = 6912.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.1526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.078  10235  Z= 0.103
  Angle     :  0.451   8.550  13809  Z= 0.240
  Chirality :  0.038   0.358   1532
  Planarity :  0.004   0.134   1786
  Dihedral  :  7.233  89.010   1524
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.90 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 22.52 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.25), residues: 1245
  helix:  1.70 (0.21), residues: 649
  sheet: -1.00 (0.40), residues: 165
  loop : -1.38 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 342 
 TYR   0.008   0.001   TYR C 324 
 PHE   0.013   0.001   PHE A 318 
 TRP   0.005   0.000   TRP A 268 
 HIS   0.005   0.001   HIS B 238 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (10223)
  covalent geometry    : angle       0.44680 (13797)
  hydrogen bonds       : bond        0.02793 (  515)
  hydrogen bonds       : angle       3.54505 ( 1539)
  metal coordination   : bond        0.00467 (   12)
  metal coordination   : angle       2.06420 (   12)

********************** 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
  140 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 128
  time to evaluate  : 0.544 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 MET cc_start: 0.8078 (tpt) cc_final: 0.7743 (tpt)
REVERT: A  350 ARG cc_start: 0.8277 (mtt180) cc_final: 0.7792 (ptp-110)
  outliers start: 12
  outliers final: 12
  residues processed: 139
  average time/residue: 0.2272
  time to fit residues: 45.4158
Evaluate side-chains
  138 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 126
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  175 GLN
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  146 GLU
Chi-restraints excluded: chain C residue  326 LEU
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  378 SER
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 0 optimal weight:   10.0000
   chunk 87 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 118 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 72 optimal weight:    3.9990
   chunk 115 optimal weight:    0.0270
   chunk 8 optimal weight:    1.9990
   chunk 103 optimal weight:    0.8980
   overall best weight:    1.1844

-------------------------------------------------------------------------------
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 = 0.3303 r_free = 0.3303 target = 0.126378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.094863 restraints weight = 34963.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.099788 restraints weight = 17091.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.102974 restraints weight = 11001.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.104960 restraints weight = 8290.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.106363 restraints weight = 6892.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.1535

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= 0.133
  Angle     :  0.465   8.638  13809  Z= 0.249
  Chirality :  0.038   0.366   1532
  Planarity :  0.004   0.134   1786
  Dihedral  :  7.260  87.139   1524
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.94 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 22.71 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.25), residues: 1245
  helix:  1.66 (0.21), residues: 651
  sheet: -0.97 (0.40), residues: 165
  loop : -1.37 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 342 
 TYR   0.009   0.001   TYR C 324 
 PHE   0.038   0.001   PHE A 318 
 TRP   0.004   0.001   TRP A 268 
 HIS   0.008   0.001   HIS B 238 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (10223)
  covalent geometry    : angle       0.46071 (13797)
  hydrogen bonds       : bond        0.02910 (  515)
  hydrogen bonds       : angle       3.58091 ( 1539)
  metal coordination   : bond        0.00622 (   12)
  metal coordination   : angle       2.20616 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3085.94 seconds
wall clock time: 53 minutes 28.94 seconds (3208.94 seconds total)