Starting phenix.real_space_refine
on Thu Jul 24 05:37:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mk2_23884/07_2025/7mk2_23884.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mk2_23884/07_2025/7mk2_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mk2_23884/07_2025/7mk2_23884.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mk2_23884/07_2025/7mk2_23884.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mk2_23884/07_2025/7mk2_23884.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mk2_23884/07_2025/7mk2_23884.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'GLU:plan': 9, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2}
          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, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP: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: 3.71, per 1000 atoms: 0.70
  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: 1.28
  Conformation dependent library (CDL) restraints added in 625.6 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: 0.59
  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: 1.29

  Time building geometry restraints manager: 1.52 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:             1.350
  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:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.920
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.460
-------------------------------------------------------------------------------
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 : 8.87
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 HIS   0.009   0.001   HIS B 334 
 PHE   0.012   0.001   PHE B  53 
 TYR   0.011   0.002   TYR B 186 
 ARG   0.005   0.000   ARG A 363 

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

*********************** 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  : 0.654 
Fit side-chains
REVERT: A   44 SER cc_start: 0.8001 (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: 0.8262 (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: 0.9012 (tt) cc_final: 0.8727 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1399
  time to fit residues: 23.7124
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  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    0.7980
   chunk 53 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0030
   chunk 28 optimal weight:    0.3980
   chunk 54 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 33 optimal weight:    0.1980
   chunk 40 optimal weight:    0.4980
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.3390

-------------------------------------------------------------------------------
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 = 0.3684 r_free = 0.3684 target = 0.162114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.141250 restraints weight = 7016.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.144315 restraints weight = 4263.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.146465 restraints weight = 2979.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.0984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5413  Z= 0.140
  Angle     :  0.647   7.717   7327  Z= 0.332
  Chirality :  0.042   0.168    902
  Planarity :  0.004   0.040    924
  Dihedral  :  4.872  22.559    750
  Min Nonbonded Distance : 2.516

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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.38 (0.31), residues: 700
  helix: -0.22 (0.25), residues: 444
  sheet:  None (None), residues: 0
  loop : -2.09 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B 290 
 PHE   0.012   0.001   PHE B  53 
 TYR   0.015   0.001   TYR B 186 
 ARG   0.002   0.000   ARG A 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04999 (  280)
  hydrogen bonds       : angle       4.81180 (  828)
  metal coordination   : bond        0.00688 (    8)
  metal coordination   : angle       2.70981 (    6)
  covalent geometry    : bond        0.00315 ( 5405)
  covalent geometry    : angle       0.64250 ( 7321)

*********************** 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  : 0.594 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8740 (mt) cc_final: 0.8199 (mt)
REVERT: A  234 MET cc_start: 0.8041 (ttp) cc_final: 0.7668 (ttm)
REVERT: A  316 LYS cc_start: 0.8214 (tmtt) cc_final: 0.7724 (tptp)
REVERT: B  208 LEU cc_start: 0.8951 (tt) cc_final: 0.8698 (tt)
  outliers start: 10
  outliers final: 8
  residues processed: 120
  average time/residue: 0.1291
  time to fit residues: 21.7036
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  : 0.767 
-------------------------------------------------------------------------------
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 58 optimal weight:    3.9990
   chunk 68 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 50 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 3 optimal weight:    0.5980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3652 r_free = 0.3652 target = 0.159061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.138104 restraints weight = 6971.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.141146 restraints weight = 4285.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.143311 restraints weight = 3006.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.1157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   5413  Z= 0.178
  Angle     :  0.641   8.158   7327  Z= 0.333
  Chirality :  0.042   0.157    902
  Planarity :  0.004   0.046    924
  Dihedral  :  4.802  21.098    750
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 16.23 %
    Favored  : 81.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.31), residues: 700
  helix: -0.24 (0.25), residues: 448
  sheet:  None (None), residues: 0
  loop : -2.13 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 300 
 PHE   0.011   0.001   PHE A  79 
 TYR   0.012   0.001   TYR B 186 
 ARG   0.002   0.000   ARG A  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05356 (  280)
  hydrogen bonds       : angle       4.75741 (  828)
  metal coordination   : bond        0.00784 (    8)
  metal coordination   : angle       2.43130 (    6)
  covalent geometry    : bond        0.00422 ( 5405)
  covalent geometry    : angle       0.63775 ( 7321)

*********************** 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
  123 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.585 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8643 (mt) cc_final: 0.8094 (mt)
REVERT: A  234 MET cc_start: 0.7904 (ttp) cc_final: 0.7198 (ttm)
REVERT: A  316 LYS cc_start: 0.8297 (tmtt) cc_final: 0.7960 (tptp)
REVERT: B   51 ASN cc_start: 0.8511 (m-40) cc_final: 0.8202 (m110)
  outliers start: 15
  outliers final: 14
  residues processed: 117
  average time/residue: 0.1333
  time to fit residues: 21.4888
Evaluate side-chains
  117 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 VAL
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 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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 3 optimal weight:    0.5980
   chunk 45 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 50 optimal weight:    0.0770
   chunk 68 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.5738

-------------------------------------------------------------------------------
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 = 0.3662 r_free = 0.3662 target = 0.159833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.138573 restraints weight = 7168.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.141814 restraints weight = 4351.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.144109 restraints weight = 3003.541|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.1296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5413  Z= 0.158
  Angle     :  0.615   7.490   7327  Z= 0.318
  Chirality :  0.041   0.159    902
  Planarity :  0.004   0.046    924
  Dihedral  :  4.716  21.872    750
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.31), residues: 700
  helix: -0.11 (0.25), residues: 438
  sheet:  None (None), residues: 0
  loop : -2.06 (0.36), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 189 
 PHE   0.009   0.001   PHE B  53 
 TYR   0.012   0.001   TYR B 186 
 ARG   0.003   0.000   ARG B 339 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04920 (  280)
  hydrogen bonds       : angle       4.60640 (  828)
  metal coordination   : bond        0.00742 (    8)
  metal coordination   : angle       2.28830 (    6)
  covalent geometry    : bond        0.00371 ( 5405)
  covalent geometry    : angle       0.61211 ( 7321)

*********************** 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
  125 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 0.583 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8630 (mt) cc_final: 0.8065 (mt)
REVERT: A  234 MET cc_start: 0.7772 (ttp) cc_final: 0.7080 (ttm)
REVERT: A  316 LYS cc_start: 0.8468 (tmtt) cc_final: 0.8248 (tptp)
REVERT: B  339 ARG cc_start: 0.8699 (tpt-90) cc_final: 0.8333 (tpt-90)
  outliers start: 19
  outliers final: 11
  residues processed: 118
  average time/residue: 0.1368
  time to fit residues: 22.1764
Evaluate side-chains
  110 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
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 A residue  262 LYS
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 52 optimal weight:    0.4980
   chunk 37 optimal weight:    0.0070
   chunk 26 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0030
   chunk 68 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.4008

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.161533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.140579 restraints weight = 6983.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.143808 restraints weight = 4200.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.146057 restraints weight = 2889.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.1499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5413  Z= 0.131
  Angle     :  0.611   9.368   7327  Z= 0.306
  Chirality :  0.040   0.149    902
  Planarity :  0.004   0.044    924
  Dihedral  :  4.546  22.421    750
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 18.85 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.31), residues: 700
  helix: -0.11 (0.25), residues: 446
  sheet:  None (None), residues: 0
  loop : -2.09 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 300 
 PHE   0.010   0.001   PHE B  53 
 TYR   0.012   0.001   TYR B 186 
 ARG   0.003   0.000   ARG B 339 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04361 (  280)
  hydrogen bonds       : angle       4.44307 (  828)
  metal coordination   : bond        0.00581 (    8)
  metal coordination   : angle       1.84664 (    6)
  covalent geometry    : bond        0.00301 ( 5405)
  covalent geometry    : angle       0.60875 ( 7321)

*********************** 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: 18
    poor density    : 106
  time to evaluate  : 0.630 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8613 (mt) cc_final: 0.8045 (mt)
REVERT: A  122 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7508 (tp30)
REVERT: A  234 MET cc_start: 0.7975 (ttp) cc_final: 0.7268 (ttm)
REVERT: B   51 ASN cc_start: 0.8503 (m-40) cc_final: 0.8205 (m110)
REVERT: B  208 LEU cc_start: 0.9080 (tt) cc_final: 0.8836 (tt)
REVERT: B  339 ARG cc_start: 0.8727 (tpt-90) cc_final: 0.8362 (tpt-90)
  outliers start: 18
  outliers final: 16
  residues processed: 116
  average time/residue: 0.1329
  time to fit residues: 21.2066
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  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 VAL
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  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  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  335 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 54 optimal weight:    0.8980
   chunk 8 optimal weight:    0.2980
   chunk 56 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 7 optimal weight:    0.0570
   chunk 48 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0370
   overall best weight:    0.3176

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.163133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.142164 restraints weight = 7001.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.145423 restraints weight = 4250.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.147709 restraints weight = 2932.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.1695

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= 0.121
  Angle     :  0.593   7.758   7327  Z= 0.299
  Chirality :  0.040   0.146    902
  Planarity :  0.004   0.042    924
  Dihedral  :  4.400  22.718    750
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 18.67 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.32), residues: 700
  helix: -0.01 (0.25), residues: 446
  sheet:  None (None), residues: 0
  loop : -1.99 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 189 
 PHE   0.017   0.001   PHE B  53 
 TYR   0.012   0.001   TYR B 186 
 ARG   0.002   0.000   ARG B 339 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04055 (  280)
  hydrogen bonds       : angle       4.32600 (  828)
  metal coordination   : bond        0.00504 (    8)
  metal coordination   : angle       1.53253 (    6)
  covalent geometry    : bond        0.00274 ( 5405)
  covalent geometry    : angle       0.59165 ( 7321)

*********************** 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
  127 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.578 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8543 (mt) cc_final: 0.8018 (mt)
REVERT: A   62 ASP cc_start: 0.8334 (t70) cc_final: 0.8062 (t0)
REVERT: A  122 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7446 (mm-30)
REVERT: A  234 MET cc_start: 0.7976 (ttp) cc_final: 0.7272 (ttm)
REVERT: A  393 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6342 (mm)
REVERT: B  208 LEU cc_start: 0.9023 (tt) cc_final: 0.8811 (tt)
REVERT: B  339 ARG cc_start: 0.8710 (tpt-90) cc_final: 0.8375 (tpt-90)
  outliers start: 23
  outliers final: 18
  residues processed: 119
  average time/residue: 0.1292
  time to fit residues: 21.3969
Evaluate side-chains
  119 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 VAL
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  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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 39 optimal weight:    0.4980
   chunk 63 optimal weight:    0.2980
   chunk 38 optimal weight:    0.7980
   chunk 32 optimal weight:    0.4980
   chunk 62 optimal weight:    1.9990
   chunk 19 optimal weight:    0.3980
   chunk 20 optimal weight:    0.3980
   chunk 42 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 = 0.3685 r_free = 0.3685 target = 0.162191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.141124 restraints weight = 6934.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.144356 restraints weight = 4211.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.146671 restraints weight = 2902.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.1737

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= 0.133
  Angle     :  0.626   9.597   7327  Z= 0.309
  Chirality :  0.040   0.142    902
  Planarity :  0.004   0.039    924
  Dihedral  :  4.359  22.095    750
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 19.20 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.32), residues: 700
  helix:  0.02 (0.25), residues: 448
  sheet:  None (None), residues: 0
  loop : -1.95 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 189 
 PHE   0.012   0.001   PHE B  53 
 TYR   0.011   0.001   TYR B 186 
 ARG   0.002   0.000   ARG B 339 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04242 (  280)
  hydrogen bonds       : angle       4.36747 (  828)
  metal coordination   : bond        0.00534 (    8)
  metal coordination   : angle       1.67296 (    6)
  covalent geometry    : bond        0.00307 ( 5405)
  covalent geometry    : angle       0.62440 ( 7321)

*********************** 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
  131 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 107
  time to evaluate  : 0.583 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8556 (mt) cc_final: 0.7999 (mt)
REVERT: A   62 ASP cc_start: 0.8354 (t70) cc_final: 0.8078 (t0)
REVERT: A  122 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7458 (mm-30)
REVERT: A  234 MET cc_start: 0.7908 (ttp) cc_final: 0.7174 (ttm)
REVERT: A  393 LEU cc_start: 0.6592 (OUTLIER) cc_final: 0.6106 (mm)
REVERT: B  339 ARG cc_start: 0.8717 (tpt-90) cc_final: 0.8358 (tpt-90)
  outliers start: 24
  outliers final: 22
  residues processed: 120
  average time/residue: 0.1287
  time to fit residues: 21.4186
Evaluate side-chains
  129 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 VAL
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
Chi-restraints excluded: chain B residue  367 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 2 optimal weight:    0.0060
   chunk 67 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 5 optimal weight:    0.5980
   chunk 60 optimal weight:    3.9990
   chunk 66 optimal weight:    0.3980
   chunk 45 optimal weight:    0.5980
   chunk 57 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 40 optimal weight:    0.0970
   overall best weight:    0.3394

-------------------------------------------------------------------------------
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 = 0.3714 r_free = 0.3714 target = 0.164861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.144023 restraints weight = 6952.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.147249 restraints weight = 4221.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.149470 restraints weight = 2909.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.1845

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= 0.122
  Angle     :  0.620   9.111   7327  Z= 0.306
  Chirality :  0.041   0.231    902
  Planarity :  0.004   0.040    924
  Dihedral  :  4.275  22.582    750
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 19.20 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.32), residues: 700
  helix:  0.07 (0.25), residues: 448
  sheet:  None (None), residues: 0
  loop : -1.91 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 189 
 PHE   0.016   0.001   PHE A  53 
 TYR   0.011   0.001   TYR B 186 
 ARG   0.003   0.000   ARG B 339 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03987 (  280)
  hydrogen bonds       : angle       4.29031 (  828)
  metal coordination   : bond        0.00457 (    8)
  metal coordination   : angle       1.50619 (    6)
  covalent geometry    : bond        0.00276 ( 5405)
  covalent geometry    : angle       0.61901 ( 7321)

*********************** 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
  132 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.574 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8538 (mt) cc_final: 0.8036 (mt)
REVERT: A   62 ASP cc_start: 0.8330 (t70) cc_final: 0.8081 (t0)
REVERT: A  122 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7545 (tp30)
REVERT: A  206 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8219 (tp)
REVERT: A  234 MET cc_start: 0.7892 (ttp) cc_final: 0.7262 (ttm)
REVERT: B   51 ASN cc_start: 0.8500 (m110) cc_final: 0.8300 (m110)
REVERT: B  339 ARG cc_start: 0.8662 (tpt-90) cc_final: 0.8307 (tpt-90)
  outliers start: 24
  outliers final: 22
  residues processed: 120
  average time/residue: 0.1302
  time to fit residues: 21.6358
Evaluate side-chains
  127 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 VAL
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 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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 46 optimal weight:    6.9990
   chunk 11 optimal weight:    0.1980
   chunk 60 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0670
   chunk 38 optimal weight:    0.5980
   chunk 28 optimal weight:    0.4980
   chunk 67 optimal weight:    0.0170
   overall best weight:    0.2756

-------------------------------------------------------------------------------
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 = 0.3713 r_free = 0.3713 target = 0.164596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.143746 restraints weight = 6929.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.146959 restraints weight = 4163.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.149236 restraints weight = 2865.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.1953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5413  Z= 0.117
  Angle     :  0.617   9.819   7327  Z= 0.303
  Chirality :  0.040   0.154    902
  Planarity :  0.003   0.041    924
  Dihedral  :  4.244  22.551    750
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 19.72 %
    Favored  : 75.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.32), residues: 700
  helix:  0.10 (0.26), residues: 448
  sheet:  None (None), residues: 0
  loop : -1.90 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS A 189 
 PHE   0.012   0.001   PHE B  53 
 TYR   0.011   0.001   TYR B 186 
 ARG   0.003   0.000   ARG B 339 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03846 (  280)
  hydrogen bonds       : angle       4.27026 (  828)
  metal coordination   : bond        0.00404 (    8)
  metal coordination   : angle       1.39067 (    6)
  covalent geometry    : bond        0.00260 ( 5405)
  covalent geometry    : angle       0.61554 ( 7321)

*********************** 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
  129 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 103
  time to evaluate  : 0.625 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8544 (mt) cc_final: 0.8041 (mt)
REVERT: A   62 ASP cc_start: 0.8352 (t70) cc_final: 0.8100 (t0)
REVERT: A  122 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7474 (mm-30)
REVERT: A  206 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8247 (tp)
REVERT: A  234 MET cc_start: 0.7712 (ttp) cc_final: 0.7085 (ttm)
REVERT: A  393 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6205 (mm)
REVERT: B   51 ASN cc_start: 0.8497 (m110) cc_final: 0.8276 (m110)
REVERT: B  339 ARG cc_start: 0.8702 (tpt-90) cc_final: 0.8373 (tpt-90)
  outliers start: 26
  outliers final: 23
  residues processed: 118
  average time/residue: 0.1237
  time to fit residues: 20.5530
Evaluate side-chains
  129 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 VAL
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  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  227 ILE
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  293 LEU
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 19 optimal weight:    0.0870
   chunk 14 optimal weight:    0.5980
   chunk 7 optimal weight:    0.0770
   chunk 20 optimal weight:    0.7980
   chunk 21 optimal weight:    0.2980
   chunk 37 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 32 optimal weight:    0.3980
   chunk 48 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.2916

-------------------------------------------------------------------------------
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 = 0.3716 r_free = 0.3716 target = 0.164936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.143917 restraints weight = 6983.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.147151 restraints weight = 4199.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.149469 restraints weight = 2885.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5413  Z= 0.120
  Angle     :  0.644  10.483   7327  Z= 0.315
  Chirality :  0.041   0.219    902
  Planarity :  0.004   0.043    924
  Dihedral  :  4.244  22.118    750
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 20.42 %
    Favored  : 75.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.32), residues: 700
  helix:  0.14 (0.26), residues: 448
  sheet:  None (None), residues: 0
  loop : -1.88 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 189 
 PHE   0.012   0.001   PHE B  53 
 TYR   0.010   0.001   TYR B 186 
 ARG   0.002   0.000   ARG B 339 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03818 (  280)
  hydrogen bonds       : angle       4.27155 (  828)
  metal coordination   : bond        0.00404 (    8)
  metal coordination   : angle       1.34197 (    6)
  covalent geometry    : bond        0.00270 ( 5405)
  covalent geometry    : angle       0.64335 ( 7321)

********************** 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
  130 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 106
  time to evaluate  : 0.566 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8538 (mt) cc_final: 0.8048 (mt)
REVERT: A   62 ASP cc_start: 0.8351 (t70) cc_final: 0.8087 (t0)
REVERT: A  122 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7544 (tp30)
REVERT: A  206 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8210 (tp)
REVERT: A  234 MET cc_start: 0.7699 (ttp) cc_final: 0.7115 (ttm)
REVERT: A  393 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6212 (mm)
REVERT: B   51 ASN cc_start: 0.8495 (m110) cc_final: 0.8255 (m110)
REVERT: B  217 MET cc_start: 0.7157 (tpp) cc_final: 0.5508 (tpt)
REVERT: B  339 ARG cc_start: 0.8743 (tpt-90) cc_final: 0.8435 (tpt-90)
  outliers start: 24
  outliers final: 21
  residues processed: 119
  average time/residue: 0.1166
  time to fit residues: 19.7505
Evaluate side-chains
  126 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 VAL
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  227 ILE
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0670
   chunk 57 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 46 optimal weight:    6.9990
   chunk 30 optimal weight:    0.0770
   chunk 16 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.4476

-------------------------------------------------------------------------------
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 = 0.3700 r_free = 0.3700 target = 0.163327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.142385 restraints weight = 6920.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.145655 restraints weight = 4165.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.147911 restraints weight = 2858.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.1999

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= 0.138
  Angle     :  0.645  10.094   7327  Z= 0.319
  Chirality :  0.041   0.157    902
  Planarity :  0.004   0.043    924
  Dihedral  :  4.288  21.333    750
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 19.90 %
    Favored  : 75.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.32), residues: 700
  helix:  0.15 (0.26), residues: 448
  sheet:  None (None), residues: 0
  loop : -1.92 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 300 
 PHE   0.010   0.001   PHE B  53 
 TYR   0.010   0.001   TYR B 186 
 ARG   0.002   0.000   ARG B 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04197 (  280)
  hydrogen bonds       : angle       4.30885 (  828)
  metal coordination   : bond        0.00573 (    8)
  metal coordination   : angle       1.54646 (    6)
  covalent geometry    : bond        0.00320 ( 5405)
  covalent geometry    : angle       0.64332 ( 7321)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1998.45 seconds
wall clock time: 35 minutes 11.35 seconds (2111.35 seconds total)