Starting phenix.real_space_refine
on Tue Mar  3 13:36:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mk2_23884/03_2026/7mk2_23884.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mk2_23884/03_2026/7mk2_23884.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mk2_23884/03_2026/7mk2_23884.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mk2_23884/03_2026/7mk2_23884.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mk2_23884/03_2026/7mk2_23884.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mk2_23884/03_2026/7mk2_23884.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.034
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: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      34      5.16       5
     C    3390      2.51       5
     N     914      2.21       5
     O     993      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5333
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2675
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 354, 2675
          Classifications: {'peptide': 354}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 11, 'TRANS': 342}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 80
          Unresolved non-hydrogen angles: 99
          Unresolved non-hydrogen dihedrals: 63
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 2, 'ASP:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 57
    Chain: "B"
      Number of atoms: 2656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 354, 2656
          Classifications: {'peptide': 354}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 11, 'TRANS': 342}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 99
          Unresolved non-hydrogen angles: 120
          Unresolved non-hydrogen dihedrals: 80
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 11, 'ASN:plan1': 2, 'ASP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 57
    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: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    832  SG  CYS A 150     111.033  43.802  42.621  1.00 46.19           S
  ATOM    868  SG  CYS A 155     110.325  45.039  46.143  1.00 47.27           S
  ATOM    902  SG  CYS A 160     108.157  46.307  43.301  1.00 39.74           S
  ATOM   3503  SG  CYS B 150      37.143  45.391  42.094  1.00 40.69           S
  ATOM   3535  SG  CYS B 155      37.704  44.225  45.629  1.00 39.08           S
  ATOM   3569  SG  CYS B 160      39.926  42.836  42.897  1.00 40.43           S

  Time building chain proxies: 1.23, per 1000 atoms: 0.23
  Number of scatterers: 5333
  At special positions: 0
  Unit cell: (149.538, 92.2383, 62.8897, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      34     16.00
     O     993      8.00
     N     914      7.00
     C    3390      6.00
    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: 0.39
  Conformation dependent library (CDL) restraints added in 262.4 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 701 "
        pdb="ZN    ZN A 701 " - pdb=" ND1 HIS A 157 "
        pdb="ZN    ZN A 701 " - pdb=" SG  CYS A 150 "
        pdb="ZN    ZN A 701 " - pdb=" SG  CYS A 160 "
        pdb="ZN    ZN A 701 " - pdb=" SG  CYS A 155 "
      pdb="  ZN B 701 "
        pdb="ZN    ZN B 701 " - pdb=" ND1 HIS B 157 "
        pdb="ZN    ZN B 701 " - pdb=" SG  CYS B 150 "
        pdb="ZN    ZN B 701 " - pdb=" SG  CYS B 155 "
        pdb="ZN    ZN B 701 " - pdb=" SG  CYS B 160 "
      Number of angles added : 6


  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1376

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 2 sheets defined
      67.2% alpha, 2.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 40 through 59
      removed outlier: 3.649A  pdb=" N   SER A  59 " --> pdb=" O   SER A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 88
      removed outlier: 3.613A  pdb=" N   LEU A  84 " --> pdb=" O   HIS A  80 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   SER A  88 " --> pdb=" O   LEU A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 99
    Processing helix  chain 'A' and resid 114 through 118
    Processing helix  chain 'A' and resid 125 through 138
    Processing helix  chain 'A' and resid 160 through 178
    Processing helix  chain 'A' and resid 179 through 194
    Processing helix  chain 'A' and resid 195 through 197
      No H-bonds generated for 'chain 'A' and resid 195 through 197'
    Processing helix  chain 'A' and resid 198 through 212
      removed outlier: 4.374A  pdb=" N   VAL A 204 " --> pdb=" O   GLU A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 215
      No H-bonds generated for 'chain 'A' and resid 213 through 215'
    Processing helix  chain 'A' and resid 216 through 230
      removed outlier: 3.934A  pdb=" N   ARG A 222 " --> pdb=" O   LYS A 218 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   SER A 230 " --> pdb=" O   ILE A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 240
      removed outlier: 3.614A  pdb=" N   LEU A 237 " --> pdb=" O   ASP A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 256
      removed outlier: 4.710A  pdb=" N   GLU A 248 " --> pdb=" O   GLU A 244 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   ASP A 251 " --> pdb=" O   LYS A 247 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ARG A 253 " --> pdb=" O   ILE A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 275
      removed outlier: 3.831A  pdb=" N   SER A 268 " --> pdb=" O   LYS A 264 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ASN A 269 " --> pdb=" O   LYS A 265 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   VAL A 270 " --> pdb=" O   HIS A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 287
    Processing helix  chain 'A' and resid 292 through 297
      removed outlier: 4.126A  pdb=" N   ALA A 296 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 306
    Processing helix  chain 'A' and resid 307 through 316
      removed outlier: 3.827A  pdb=" N   LYS A 316 " --> pdb=" O   THR A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 340
      removed outlier: 3.903A  pdb=" N   LYS A 340 " --> pdb=" O   ALA A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 352
    Processing helix  chain 'A' and resid 364 through 372
      removed outlier: 3.510A  pdb=" N   ILE A 368 " --> pdb=" O   THR A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 400
      removed outlier: 3.567A  pdb=" N   CYS A 394 " --> pdb=" O   LYS A 390 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   VAL A 395 " --> pdb=" O   GLY A 391 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   GLU A 396 " --> pdb=" O   ARG A 392 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ILE A 397 " --> pdb=" O   LEU A 393 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLN A 400 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 59
      removed outlier: 3.719A  pdb=" N   ALA B  45 " --> pdb=" O   PRO B  41 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU B  46 " --> pdb=" O   ASP B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 87
      removed outlier: 3.711A  pdb=" N   LEU B  84 " --> pdb=" O   HIS B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 101
      removed outlier: 3.515A  pdb=" N   LYS B  92 " --> pdb=" O   SER B  88 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   LYS B 100 " --> pdb=" O   ALA B  96 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   GLU B 101 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 138
    Processing helix  chain 'B' and resid 160 through 178
    Processing helix  chain 'B' and resid 179 through 194
    Processing helix  chain 'B' and resid 198 through 212
      removed outlier: 4.707A  pdb=" N   VAL B 204 " --> pdb=" O   GLU B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 215
      No H-bonds generated for 'chain 'B' and resid 213 through 215'
    Processing helix  chain 'B' and resid 216 through 229
      removed outlier: 3.767A  pdb=" N   LYS B 229 " --> pdb=" O   GLU B 225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 240
      removed outlier: 3.705A  pdb=" N   SER B 240 " --> pdb=" O   SER B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 254
      removed outlier: 3.837A  pdb=" N   ARG B 252 " --> pdb=" O   GLU B 248 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   LYS B 254 " --> pdb=" O   ILE B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 275
      removed outlier: 3.954A  pdb=" N   ASN B 269 " --> pdb=" O   LYS B 265 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   VAL B 270 " --> pdb=" O   HIS B 266 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 290
    Processing helix  chain 'B' and resid 292 through 296
    Processing helix  chain 'B' and resid 297 through 305
    Processing helix  chain 'B' and resid 307 through 317
    Processing helix  chain 'B' and resid 331 through 340
      removed outlier: 3.546A  pdb=" N   VAL B 335 " --> pdb=" O   THR B 331 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LYS B 340 " --> pdb=" O   ALA B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 341 through 351
    Processing helix  chain 'B' and resid 364 through 373
      removed outlier: 3.502A  pdb=" N   THR B 373 " --> pdb=" O   ALA B 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 389 through 398
      removed outlier: 3.500A  pdb=" N   LEU B 393 " --> pdb=" O   LEU B 389 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL B 395 " --> pdb=" O   GLY B 391 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   GLU B 396 " --> pdb=" O   ARG B 392 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ILE B 397 " --> pdb=" O   LEU B 393 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LEU B 398 " --> pdb=" O   CYS B 394 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79
    Processing sheet with id=AA2, first strand: chain 'B' and resid 76 through 79
      removed outlier: 6.749A  pdb=" N   LYS B  68 " --> pdb=" O   LEU B 112 " (cutoff:3.500A)

    280 hydrogen bonds defined for protein.
    828 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: 0.70

  Time building geometry restraints manager: 0.52 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1759
        1.34 -     1.46: 848
        1.46 -     1.57: 2752
        1.57 -     1.69: 0
        1.69 -     1.81: 46
  Bond restraints: 5405
  Sorted by residual:
  bond pdb=" C   VAL A 260 "
       pdb=" N   PRO A 261 "
    ideal  model  delta    sigma   weight residual
    1.334  1.369 -0.035 2.34e-02 1.83e+03 2.22e+00
  bond pdb=" CG1 ILE A 183 "
       pdb=" CD1 ILE A 183 "
    ideal  model  delta    sigma   weight residual
    1.513  1.459  0.054 3.90e-02 6.57e+02 1.91e+00
  bond pdb=" CG1 ILE B 183 "
       pdb=" CD1 ILE B 183 "
    ideal  model  delta    sigma   weight residual
    1.513  1.460  0.053 3.90e-02 6.57e+02 1.82e+00
  bond pdb=" CB  MET A 367 "
       pdb=" CG  MET A 367 "
    ideal  model  delta    sigma   weight residual
    1.520  1.487  0.033 3.00e-02 1.11e+03 1.23e+00
  bond pdb=" CB  CYS A 223 "
       pdb=" SG  CYS A 223 "
    ideal  model  delta    sigma   weight residual
    1.808  1.773  0.035 3.30e-02 9.18e+02 1.13e+00
  ... (remaining 5400 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 7049
        1.58 -     3.15: 226
        3.15 -     4.73: 33
        4.73 -     6.30: 12
        6.30 -     7.88: 1
  Bond angle restraints: 7321
  Sorted by residual:
  angle pdb=" N   VAL A 158 "
        pdb=" CA  VAL A 158 "
        pdb=" C   VAL A 158 "
      ideal   model   delta    sigma   weight residual
     113.53  110.41    3.12 9.80e-01 1.04e+00 1.01e+01
  angle pdb=" C   SER B 276 "
        pdb=" N   ASP B 277 "
        pdb=" CA  ASP B 277 "
      ideal   model   delta    sigma   weight residual
     121.54  127.46   -5.92 1.91e+00 2.74e-01 9.61e+00
  angle pdb=" C   GLU B 149 "
        pdb=" N   CYS B 150 "
        pdb=" CA  CYS B 150 "
      ideal   model   delta    sigma   weight residual
     121.54  115.97    5.57 1.91e+00 2.74e-01 8.49e+00
  angle pdb=" C   VAL B 164 "
        pdb=" N   ASP B 165 "
        pdb=" CA  ASP B 165 "
      ideal   model   delta    sigma   weight residual
     121.14  116.30    4.84 1.75e+00 3.27e-01 7.64e+00
  angle pdb=" N   VAL B 194 "
        pdb=" CA  VAL B 194 "
        pdb=" C   VAL B 194 "
      ideal   model   delta    sigma   weight residual
     109.34  114.40   -5.06 2.08e+00 2.31e-01 5.92e+00
  ... (remaining 7316 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.99: 2984
       16.99 -    33.98: 294
       33.98 -    50.98: 61
       50.98 -    67.97: 9
       67.97 -    84.96: 3
  Dihedral angle restraints: 3351
    sinusoidal: 1255
      harmonic: 2096
  Sorted by residual:
  dihedral pdb=" CA  LYS B 119 "
           pdb=" C   LYS B 119 "
           pdb=" N   ASP B 120 "
           pdb=" CA  ASP B 120 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.59  -17.41     0      5.00e+00 4.00e-02 1.21e+01
  dihedral pdb=" CG  ARG B  87 "
           pdb=" CD  ARG B  87 "
           pdb=" NE  ARG B  87 "
           pdb=" CZ  ARG B  87 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  136.94   43.06     2      1.50e+01 4.44e-03 9.95e+00
  dihedral pdb=" CA  GLU B 149 "
           pdb=" C   GLU B 149 "
           pdb=" N   CYS B 150 "
           pdb=" CA  CYS B 150 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.29  -15.71     0      5.00e+00 4.00e-02 9.87e+00
  ... (remaining 3348 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 561
       0.036 -    0.071: 258
       0.071 -    0.107: 62
       0.107 -    0.143: 19
       0.143 -    0.178: 2
  Chirality restraints: 902
  Sorted by residual:
  chirality pdb=" CA  MET B 367 "
            pdb=" N   MET B 367 "
            pdb=" C   MET B 367 "
            pdb=" CB  MET B 367 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.95e-01
  chirality pdb=" CA  ASP B 277 "
            pdb=" N   ASP B 277 "
            pdb=" C   ASP B 277 "
            pdb=" CB  ASP B 277 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.16e-01
  chirality pdb=" CA  ASP B 165 "
            pdb=" N   ASP B 165 "
            pdb=" C   ASP B 165 "
            pdb=" CB  ASP B 165 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.59e-01
  ... (remaining 899 not shown)

  Planarity restraints: 924
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 141 "   -0.027 5.00e-02 4.00e+02   4.18e-02 2.79e+00
        pdb=" N   PRO B 142 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO B 142 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 142 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 260 "    0.026 5.00e-02 4.00e+02   3.96e-02 2.51e+00
        pdb=" N   PRO B 261 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B 261 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 261 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B  59 "   -0.025 5.00e-02 4.00e+02   3.71e-02 2.21e+00
        pdb=" N   PRO B  60 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO B  60 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B  60 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 921 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 954
        2.76 -     3.30: 5420
        3.30 -     3.83: 8140
        3.83 -     4.37: 9041
        4.37 -     4.90: 15462
  Nonbonded interactions: 39017
  Sorted by model distance:
  nonbonded pdb=" O   VAL B 303 "
            pdb=" NH1 ARG B 339 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" OD1 ASP B 152 "
            pdb=" N   GLU B 153 "
     model   vdw
     2.271 3.120
  nonbonded pdb=" O   ASN B 307 "
            pdb=" OG1 THR B 310 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O   SER B 138 "
            pdb=" OG  SER B 138 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" NH2 ARG B 325 "
            pdb=" OE2 GLU B 357 "
     model   vdw
     2.303 3.120
  ... (remaining 39012 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 40 through 144 or (resid 145 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 146 through 152 or (resid 153 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 154 through 258 or (resid 2 \ 
59 and (name N or name CA or name C or name O or name CB )) or resid 260 through \ 
 261 or (resid 262 through 264 and (name N or name CA or name C or name O or nam \ 
e CB )) or resid 265 through 285 or (resid 286 and (name N or name CA or name C  \ 
or name O or name CB )) or resid 287 through 350 or (resid 351 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 352 through 389 or (resid 390 a \ 
nd (name N or name CA or name C or name O or name CB )) or resid 391 through 395 \ 
 or (resid 396 and (name N or name CA or name C or name O or name CB )) or resid \ 
 397 or (resid 398 through 402 and (name N or name CA or name C or name O or nam \ 
e CB )) or resid 701))
  selection = (chain 'B' and (resid 40 through 243 or (resid 244 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 245 through 286 or (resid 287 and (name N o \ 
r name CA or name C or name O or name CB or name CG )) or resid 288 through 340  \ 
or (resid 341 and (name N or name CA or name C or name O or name CB )) or resid  \ 
342 through 399 or (resid 400 through 402 and (name N or name CA or name C or na \ 
me O or name CB )) or resid 701))
}

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:             1.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.740
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
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   0.054   5413  Z= 0.192
  Angle     :  0.696   7.876   7327  Z= 0.382
  Chirality :  0.044   0.178    902
  Planarity :  0.004   0.042    924
  Dihedral  : 14.228  84.962   1975
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.60 (0.32), residues: 700
  helix: -0.28 (0.26), residues: 416
  sheet:  None (None), residues: 0
  loop : -2.22 (0.36), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 363 
 TYR   0.011   0.002   TYR B 186 
 PHE   0.012   0.001   PHE B  53 
 HIS   0.009   0.001   HIS B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 5405)
  covalent geometry    : angle       0.69240 ( 7321)
  hydrogen bonds       : bond        0.15404 (  280)
  hydrogen bonds       : angle       6.16568 (  828)
  metal coordination   : bond        0.01375 (    8)
  metal coordination   : angle       2.42048 (    6)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A   44 SER cc_start: 0.8000 (p) cc_final: 0.7726 (p)
REVERT: A   48 LEU cc_start: 0.8885 (mt) cc_final: 0.8294 (mt)
REVERT: A  234 MET cc_start: 0.7907 (ttp) cc_final: 0.7351 (ttm)
REVERT: A  316 LYS cc_start: 0.8263 (tmtt) cc_final: 0.7868 (tptp)
REVERT: B   51 ASN cc_start: 0.8623 (m110) cc_final: 0.8259 (m110)
REVERT: B  208 LEU cc_start: 0.9013 (tt) cc_final: 0.8727 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.0575
  time to fit residues: 9.8148
Evaluate side-chains
  98 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0980
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0570
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.4980
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.3498

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

Flipped N/Q/H residues before XYZ refinement:
B 189 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.161867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.140861 restraints weight = 7077.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.144007 restraints weight = 4335.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.146243 restraints weight = 3020.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.147729 restraints weight = 2307.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.148564 restraints weight = 1898.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.0986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5413  Z= 0.140
  Angle     :  0.647   7.741   7327  Z= 0.332
  Chirality :  0.042   0.168    902
  Planarity :  0.004   0.040    924
  Dihedral  :  4.875  22.521    750
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 12.22 %
    Favored  : 86.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.39 (0.31), residues: 700
  helix: -0.23 (0.25), residues: 444
  sheet:  None (None), residues: 0
  loop : -2.09 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 139 
 TYR   0.015   0.001   TYR B 186 
 PHE   0.012   0.001   PHE A  79 
 HIS   0.003   0.001   HIS B 290 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 5405)
  covalent geometry    : angle       0.64257 ( 7321)
  hydrogen bonds       : bond        0.05035 (  280)
  hydrogen bonds       : angle       4.81162 (  828)
  metal coordination   : bond        0.00680 (    8)
  metal coordination   : angle       2.71684 (    6)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8755 (mt) cc_final: 0.8212 (mt)
REVERT: A  234 MET cc_start: 0.8037 (ttp) cc_final: 0.7658 (ttm)
REVERT: A  316 LYS cc_start: 0.8196 (tmtt) cc_final: 0.7719 (tptp)
REVERT: B  208 LEU cc_start: 0.8946 (tt) cc_final: 0.8600 (tt)
  outliers start: 10
  outliers final: 8
  residues processed: 120
  average time/residue: 0.0494
  time to fit residues: 8.4601
Evaluate side-chains
  112 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 CYS
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  227 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0040
   chunk 62 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0010
   chunk 68 optimal weight:    0.8980
   chunk 30 optimal weight:    0.4980
   chunk 9 optimal weight:    0.7980
   chunk 61 optimal weight:    0.4980
   chunk 24 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.3398

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

Flipped N/Q/H residues before XYZ refinement:
B  51 ASN
B 187 GLN
B 189 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.162294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.141370 restraints weight = 6974.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.144582 restraints weight = 4230.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.146851 restraints weight = 2920.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.148268 restraints weight = 2203.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.149402 restraints weight = 1820.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.1303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5413  Z= 0.127
  Angle     :  0.585   7.631   7327  Z= 0.304
  Chirality :  0.041   0.155    902
  Planarity :  0.004   0.042    924
  Dihedral  :  4.596  22.751    750
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 16.23 %
    Favored  : 82.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.25 (0.32), residues: 700
  helix: -0.12 (0.25), residues: 448
  sheet:  None (None), residues: 0
  loop : -2.05 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  75 
 TYR   0.013   0.001   TYR B 186 
 PHE   0.010   0.001   PHE A  79 
 HIS   0.002   0.001   HIS A 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 5405)
  covalent geometry    : angle       0.58332 ( 7321)
  hydrogen bonds       : bond        0.04379 (  280)
  hydrogen bonds       : angle       4.54261 (  828)
  metal coordination   : bond        0.00500 (    8)
  metal coordination   : angle       1.85179 (    6)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.197 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8623 (mt) cc_final: 0.8051 (mt)
REVERT: A  234 MET cc_start: 0.7946 (ttp) cc_final: 0.7323 (ttm)
REVERT: A  316 LYS cc_start: 0.8268 (tmtt) cc_final: 0.7963 (tptp)
REVERT: B   51 ASN cc_start: 0.8456 (m-40) cc_final: 0.8170 (m110)
REVERT: B  208 LEU cc_start: 0.9014 (tt) cc_final: 0.8777 (tt)
  outliers start: 10
  outliers final: 10
  residues processed: 115
  average time/residue: 0.0470
  time to fit residues: 7.9491
Evaluate side-chains
  111 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 CYS
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain B residue  315 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 61 optimal weight:    0.5980
   chunk 14 optimal weight:    0.5980
   chunk 63 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 50 optimal weight:    0.4980
   chunk 52 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 187 GLN
B 189 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.160769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.139852 restraints weight = 6950.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.142936 restraints weight = 4275.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.145119 restraints weight = 2990.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.146596 restraints weight = 2290.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.147428 restraints weight = 1881.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.1377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   5413  Z= 0.169
  Angle     :  0.638   9.109   7327  Z= 0.324
  Chirality :  0.042   0.158    902
  Planarity :  0.004   0.043    924
  Dihedral  :  4.622  21.317    750
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.00 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 17.45 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.31), residues: 700
  helix: -0.14 (0.25), residues: 446
  sheet:  None (None), residues: 0
  loop : -2.12 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  75 
 TYR   0.011   0.001   TYR B 186 
 PHE   0.012   0.001   PHE B  53 
 HIS   0.004   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 5405)
  covalent geometry    : angle       0.63493 ( 7321)
  hydrogen bonds       : bond        0.04977 (  280)
  hydrogen bonds       : angle       4.60689 (  828)
  metal coordination   : bond        0.00767 (    8)
  metal coordination   : angle       2.18536 (    6)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8597 (mt) cc_final: 0.8047 (mt)
REVERT: A  234 MET cc_start: 0.7888 (ttp) cc_final: 0.7183 (ttm)
  outliers start: 21
  outliers final: 14
  residues processed: 120
  average time/residue: 0.0589
  time to fit residues: 9.8638
Evaluate side-chains
  118 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 CYS
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  262 LYS
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  117 ILE
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain B residue  315 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 52 optimal weight:    0.3980
   chunk 2 optimal weight:    0.5980
   chunk 65 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0030
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.4990

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

Flipped N/Q/H residues before XYZ refinement:
B  51 ASN
B 187 GLN
B 189 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.161349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.140170 restraints weight = 7136.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.143362 restraints weight = 4348.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.145641 restraints weight = 3010.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.147130 restraints weight = 2292.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.148204 restraints weight = 1878.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.1530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5413  Z= 0.146
  Angle     :  0.629   8.475   7327  Z= 0.315
  Chirality :  0.041   0.144    902
  Planarity :  0.004   0.042    924
  Dihedral  :  4.562  22.021    750
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 18.67 %
    Favored  : 78.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.25 (0.31), residues: 700
  helix: -0.09 (0.25), residues: 446
  sheet:  None (None), residues: 0
  loop : -2.10 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  75 
 TYR   0.011   0.001   TYR B 186 
 PHE   0.012   0.001   PHE B  53 
 HIS   0.003   0.001   HIS A 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 5405)
  covalent geometry    : angle       0.62719 ( 7321)
  hydrogen bonds       : bond        0.04611 (  280)
  hydrogen bonds       : angle       4.49860 (  828)
  metal coordination   : bond        0.00628 (    8)
  metal coordination   : angle       1.97633 (    6)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.202 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8589 (mt) cc_final: 0.8026 (mt)
REVERT: A  122 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7496 (tp30)
REVERT: A  234 MET cc_start: 0.7881 (ttp) cc_final: 0.7163 (ttm)
REVERT: B   51 ASN cc_start: 0.8482 (m-40) cc_final: 0.8188 (m110)
REVERT: B  165 ASP cc_start: 0.7320 (p0) cc_final: 0.7091 (p0)
REVERT: B  208 LEU cc_start: 0.9104 (tt) cc_final: 0.8854 (tt)
  outliers start: 19
  outliers final: 16
  residues processed: 116
  average time/residue: 0.0600
  time to fit residues: 9.6606
Evaluate side-chains
  117 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 CYS
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain B residue   55 SER
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  335 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 187 GLN
B 189 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.159006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.138061 restraints weight = 7099.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.141261 restraints weight = 4312.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.143367 restraints weight = 2983.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.144916 restraints weight = 2278.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.145866 restraints weight = 1878.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.1530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   5413  Z= 0.187
  Angle     :  0.664   9.037   7327  Z= 0.335
  Chirality :  0.042   0.156    902
  Planarity :  0.004   0.044    924
  Dihedral  :  4.670  21.072    750
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 19.02 %
    Favored  : 77.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.19 (0.31), residues: 700
  helix: -0.07 (0.25), residues: 440
  sheet:  None (None), residues: 0
  loop : -1.99 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 253 
 TYR   0.011   0.001   TYR B 186 
 PHE   0.009   0.001   PHE B  53 
 HIS   0.004   0.001   HIS A 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 5405)
  covalent geometry    : angle       0.66023 ( 7321)
  hydrogen bonds       : bond        0.05248 (  280)
  hydrogen bonds       : angle       4.62666 (  828)
  metal coordination   : bond        0.00927 (    8)
  metal coordination   : angle       2.55200 (    6)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8603 (mt) cc_final: 0.8042 (mt)
REVERT: A   62 ASP cc_start: 0.8417 (t70) cc_final: 0.8130 (t0)
REVERT: A  122 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7482 (mm-30)
REVERT: A  234 MET cc_start: 0.7560 (ttp) cc_final: 0.6999 (ttm)
  outliers start: 20
  outliers final: 17
  residues processed: 118
  average time/residue: 0.0517
  time to fit residues: 8.5280
Evaluate side-chains
  118 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 CYS
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  262 LYS
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain B residue  315 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 21 optimal weight:    0.4980
   chunk 58 optimal weight:    0.6980
   chunk 40 optimal weight:    0.5980
   chunk 15 optimal weight:    0.8980
   chunk 36 optimal weight:    0.5980
   chunk 52 optimal weight:    0.6980
   chunk 60 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 189 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.159536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.138524 restraints weight = 7040.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.141735 restraints weight = 4276.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.143966 restraints weight = 2957.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.145406 restraints weight = 2250.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.146525 restraints weight = 1850.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.1601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5413  Z= 0.166
  Angle     :  0.642  10.089   7327  Z= 0.325
  Chirality :  0.042   0.163    902
  Planarity :  0.004   0.043    924
  Dihedral  :  4.633  21.705    750
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 19.90 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.31), residues: 700
  helix: -0.08 (0.25), residues: 440
  sheet:  None (None), residues: 0
  loop : -1.98 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 253 
 TYR   0.013   0.001   TYR B 186 
 PHE   0.010   0.001   PHE B  53 
 HIS   0.004   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 5405)
  covalent geometry    : angle       0.63837 ( 7321)
  hydrogen bonds       : bond        0.04905 (  280)
  hydrogen bonds       : angle       4.56516 (  828)
  metal coordination   : bond        0.00845 (    8)
  metal coordination   : angle       2.37463 (    6)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8599 (mt) cc_final: 0.8032 (mt)
REVERT: A   62 ASP cc_start: 0.8423 (t70) cc_final: 0.8129 (t0)
REVERT: A  122 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7499 (mm-30)
REVERT: A  234 MET cc_start: 0.7556 (ttp) cc_final: 0.6992 (ttm)
REVERT: A  393 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6473 (mm)
  outliers start: 24
  outliers final: 21
  residues processed: 117
  average time/residue: 0.0540
  time to fit residues: 8.8182
Evaluate side-chains
  125 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue   82 CYS
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  262 LYS
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  335 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0970
   chunk 38 optimal weight:    0.5980
   chunk 49 optimal weight:    0.0980
   chunk 24 optimal weight:    0.9980
   chunk 59 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
B 189 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.161584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.140796 restraints weight = 6949.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.143929 restraints weight = 4214.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.146119 restraints weight = 2922.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.147684 restraints weight = 2224.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.148518 restraints weight = 1827.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5413  Z= 0.134
  Angle     :  0.628  10.734   7327  Z= 0.311
  Chirality :  0.041   0.158    902
  Planarity :  0.004   0.041    924
  Dihedral  :  4.494  22.778    750
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 20.42 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.08 (0.32), residues: 700
  helix:  0.02 (0.25), residues: 440
  sheet:  None (None), residues: 0
  loop : -1.95 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 339 
 TYR   0.012   0.001   TYR B 186 
 PHE   0.012   0.001   PHE B  53 
 HIS   0.003   0.001   HIS A 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 5405)
  covalent geometry    : angle       0.62573 ( 7321)
  hydrogen bonds       : bond        0.04295 (  280)
  hydrogen bonds       : angle       4.43939 (  828)
  metal coordination   : bond        0.00588 (    8)
  metal coordination   : angle       1.88964 (    6)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
REVERT: A   48 LEU cc_start: 0.8572 (mt) cc_final: 0.8008 (mt)
REVERT: A   62 ASP cc_start: 0.8361 (t70) cc_final: 0.8082 (t0)
REVERT: A  234 MET cc_start: 0.7554 (ttp) cc_final: 0.6977 (ttm)
  outliers start: 23
  outliers final: 22
  residues processed: 118
  average time/residue: 0.0631
  time to fit residues: 10.1980
Evaluate side-chains
  123 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 CYS
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  262 LYS
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  335 VAL
Chi-restraints excluded: chain B residue  366 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 66 optimal weight:    0.0270
   chunk 20 optimal weight:    0.8980
   chunk 47 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 69 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.5238

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

Flipped N/Q/H residues before XYZ refinement:
B 189 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.160604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.139863 restraints weight = 7067.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.143043 restraints weight = 4283.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.145266 restraints weight = 2954.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.146836 restraints weight = 2242.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.147674 restraints weight = 1828.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.1766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5413  Z= 0.150
  Angle     :  0.656  11.377   7327  Z= 0.323
  Chirality :  0.043   0.223    902
  Planarity :  0.004   0.042    924
  Dihedral  :  4.498  22.306    750
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 20.59 %
    Favored  : 74.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.04 (0.31), residues: 700
  helix:  0.06 (0.25), residues: 440
  sheet:  None (None), residues: 0
  loop : -1.93 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 253 
 TYR   0.012   0.001   TYR B 186 
 PHE   0.011   0.001   PHE B  53 
 HIS   0.003   0.001   HIS A 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 5405)
  covalent geometry    : angle       0.65429 ( 7321)
  hydrogen bonds       : bond        0.04611 (  280)
  hydrogen bonds       : angle       4.50020 (  828)
  metal coordination   : bond        0.00651 (    8)
  metal coordination   : angle       1.89607 (    6)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 100
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8580 (mt) cc_final: 0.8021 (mt)
REVERT: A   62 ASP cc_start: 0.8368 (t70) cc_final: 0.8099 (t0)
REVERT: A  122 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7413 (tp30)
REVERT: A  206 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8144 (tp)
REVERT: A  234 MET cc_start: 0.7550 (ttp) cc_final: 0.6969 (ttm)
REVERT: A  393 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6387 (mm)
REVERT: B   51 ASN cc_start: 0.8476 (m110) cc_final: 0.8166 (m110)
  outliers start: 26
  outliers final: 24
  residues processed: 119
  average time/residue: 0.0547
  time to fit residues: 9.2985
Evaluate side-chains
  129 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 103
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 CYS
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  216 CYS
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  262 LYS
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  335 VAL
Chi-restraints excluded: chain B residue  366 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 48 optimal weight:    0.4980
   chunk 5 optimal weight:    0.5980
   chunk 55 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 69 optimal weight:    0.3980
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
B 189 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.160726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.139912 restraints weight = 7041.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.143077 restraints weight = 4257.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.145299 restraints weight = 2936.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.146841 restraints weight = 2232.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.147788 restraints weight = 1822.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.1776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5413  Z= 0.152
  Angle     :  0.662  11.853   7327  Z= 0.326
  Chirality :  0.042   0.163    902
  Planarity :  0.004   0.044    924
  Dihedral  :  4.501  22.276    750
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 20.42 %
    Favored  : 74.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.32), residues: 700
  helix:  0.06 (0.25), residues: 440
  sheet:  None (None), residues: 0
  loop : -1.92 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 325 
 TYR   0.012   0.001   TYR B 186 
 PHE   0.011   0.001   PHE B  53 
 HIS   0.003   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 5405)
  covalent geometry    : angle       0.65992 ( 7321)
  hydrogen bonds       : bond        0.04611 (  280)
  hydrogen bonds       : angle       4.51216 (  828)
  metal coordination   : bond        0.00657 (    8)
  metal coordination   : angle       1.89155 (    6)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 102
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8578 (mt) cc_final: 0.8018 (mt)
REVERT: A   62 ASP cc_start: 0.8372 (t70) cc_final: 0.8103 (t0)
REVERT: A  122 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7488 (mm-30)
REVERT: A  206 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8154 (tp)
REVERT: A  234 MET cc_start: 0.7542 (ttp) cc_final: 0.6949 (ttm)
REVERT: A  393 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6255 (mm)
  outliers start: 27
  outliers final: 24
  residues processed: 122
  average time/residue: 0.0476
  time to fit residues: 8.5150
Evaluate side-chains
  125 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 99
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 CYS
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  262 LYS
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  127 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  335 VAL
Chi-restraints excluded: chain B residue  366 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 66 optimal weight:    0.4980
   chunk 19 optimal weight:    0.3980
   chunk 46 optimal weight:    5.9990
   chunk 1 optimal weight:    0.3980
   chunk 58 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0980
   chunk 33 optimal weight:    0.8980
   chunk 50 optimal weight:    0.4980
   chunk 31 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
B 189 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.162439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.141393 restraints weight = 7009.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.144700 restraints weight = 4186.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.146860 restraints weight = 2858.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.148579 restraints weight = 2170.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.149615 restraints weight = 1762.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5413  Z= 0.130
  Angle     :  0.646  11.694   7327  Z= 0.317
  Chirality :  0.041   0.161    902
  Planarity :  0.004   0.042    924
  Dihedral  :  4.413  22.795    750
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 21.12 %
    Favored  : 74.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.32), residues: 700
  helix:  0.05 (0.25), residues: 448
  sheet:  None (None), residues: 0
  loop : -1.95 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 325 
 TYR   0.012   0.001   TYR B 186 
 PHE   0.012   0.001   PHE B  53 
 HIS   0.003   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 5405)
  covalent geometry    : angle       0.64492 ( 7321)
  hydrogen bonds       : bond        0.04141 (  280)
  hydrogen bonds       : angle       4.40742 (  828)
  metal coordination   : bond        0.00541 (    8)
  metal coordination   : angle       1.67874 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 966.16 seconds
wall clock time: 17 minutes 20.06 seconds (1040.06 seconds total)