Starting phenix.real_space_refine
on Sun May  3 09:13:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mxu_48723/05_2026/9mxu_48723.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mxu_48723/05_2026/9mxu_48723.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mxu_48723/05_2026/9mxu_48723.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mxu_48723/05_2026/9mxu_48723.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mxu_48723/05_2026/9mxu_48723.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mxu_48723/05_2026/9mxu_48723.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.101
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
     S      56      5.16       5
     C    5713      2.51       5
     N    1576      2.21       5
     O    1662      1.98       5
     H    2856      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11863
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 5474
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 381, 5474
          Classifications: {'peptide': 381}
          Link IDs: {'PTRANS': 14, 'TRANS': 366}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 334
          Unresolved non-hydrogen angles: 441
          Unresolved non-hydrogen dihedrals: 298
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'TRP:plan': 7, 'GLU:plan': 9, 'GLN:plan1': 5, 'ARG:plan': 7, 'TYR:plan': 4, 'ASP:plan': 6, 'PHE:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 238
    Chain: "P"
      Number of atoms: 470
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 470
          Classifications: {'peptide': 29}
          Modifications used: {'NH3': 1}
          Link IDs: {'TRANS': 28}
    Chain: "A"
      Number of atoms: 1929
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1929
          Classifications: {'peptide': 233}
          Link IDs: {'PTRANS': 6, 'TRANS': 226}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 429
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
  Time building chain proxies: 1.94, per 1000 atoms: 0.16
  Number of scatterers: 11863
  At special positions: 0
  Unit cell: (82.45, 100.3, 174.25, 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)
     S      56     16.00
     O    1662      8.00
     N    1576      7.00
     C    5713      6.00
     H    2856      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  46 " - pdb=" SG  CYS R  71 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  62 " - pdb=" SG  CYS R 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  85 " - pdb=" SG  CYS R 126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 226 " - pdb=" SG  CYS R 296 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.81
  Conformation dependent library (CDL) restraints added in 380.0 milliseconds
  

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2194

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 11 sheets defined
      45.3% alpha, 18.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'R' and resid 31 through 50
      removed outlier: 3.809A  pdb=" N   LEU R  50 " --> pdb=" O   CYS R  46 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 89 through 95
      removed outlier: 3.953A  pdb=" N   VAL R  95 " --> pdb=" O   TRP R  91 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 123 through 127
      removed outlier: 3.778A  pdb=" N   CYS R 126 " --> pdb=" O   LEU R 123 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 169
      removed outlier: 3.826A  pdb=" N   ILE R 161 " --> pdb=" O   SER R 157 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 170 through 173
    Processing helix  chain 'R' and resid 174 through 205
      removed outlier: 3.586A  pdb=" N   ILE R 179 " --> pdb=" O   THR R 175 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 210 through 223
      removed outlier: 4.191A  pdb=" N   TRP R 214 " --> pdb=" O   GLN R 210 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ASP R 215 " --> pdb=" O   GLN R 211 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LEU R 218 " --> pdb=" O   TRP R 214 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 224 through 256
      removed outlier: 4.082A  pdb=" N   PHE R 230 " --> pdb=" O   CYS R 226 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 261 through 291
      Proline residue:  R 277  - end of helix
      Proline residue:  R 283  - end of helix
    Processing helix  chain 'R' and resid 294 through 298
    Processing helix  chain 'R' and resid 302 through 337
      removed outlier: 3.632A  pdb=" N   TRP R 306 " --> pdb=" O   ASN R 302 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ILE R 308 " --> pdb=" O   ASN R 304 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ILE R 309 " --> pdb=" O   TYR R 305 " (cutoff:3.500A)
      Proline residue:  R 312  - end of helix
    Processing helix  chain 'R' and resid 346 through 361
      removed outlier: 4.159A  pdb=" N   ALA R 350 " --> pdb=" O   LYS R 346 " (cutoff:3.500A)
      Proline residue:  R 358  - end of helix
    Processing helix  chain 'R' and resid 362 through 368
      removed outlier: 3.869A  pdb=" N   ILE R 366 " --> pdb=" O   HIS R 363 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 376 through 404
      removed outlier: 3.557A  pdb=" N   PHE R 393 " --> pdb=" O   SER R 389 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   GLY R 395 " --> pdb=" O   THR R 391 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   LEU R 396 " --> pdb=" O   SER R 392 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 406 through 416
      removed outlier: 4.608A  pdb=" N   GLU R 412 " --> pdb=" O   GLU R 408 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 2 through 29
    Processing helix  chain 'A' and resid 12 through 40
      removed outlier: 3.601A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 60
      removed outlier: 3.605A  pdb=" N   LYS A  58 " --> pdb=" O   ASN A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.616A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 253
      removed outlier: 4.019A  pdb=" N   TYR A 253 " --> pdb=" O   SER A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 279 through 283
      removed outlier: 3.980A  pdb=" N   ARG A 283 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 304
      removed outlier: 3.532A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 318
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.902A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 26
      removed outlier: 3.650A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 8 through 24
      removed outlier: 3.588A  pdb=" N   MET G  21 " --> pdb=" O   GLU G  17 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 43
      removed outlier: 3.538A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 44 through 48
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'R' and resid 101 through 102
    Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 214
      removed outlier: 4.276A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.922A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.459A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 6.079A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.998A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51
      removed outlier: 3.945A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.022A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.789A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.375A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.605A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.798A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.595A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.132A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.416A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.810A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'N' and resid 58 through 60
      removed outlier: 5.483A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)

    474 hydrogen bonds defined for protein.
    1305 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: 1.96

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 2851
        1.03 -     1.23: 7
        1.23 -     1.42: 3947
        1.42 -     1.62: 5172
        1.62 -     1.81: 76
  Bond restraints: 12053
  Sorted by residual:
  bond pdb=" CA  SER B 316 "
       pdb=" CB  SER B 316 "
    ideal  model  delta    sigma   weight residual
    1.532  1.480  0.052 1.57e-02 4.06e+03 1.08e+01
  bond pdb=" N   ARG N  98 "
       pdb=" CA  ARG N  98 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.032 1.23e-02 6.61e+03 6.84e+00
  bond pdb=" N   ASP A 343 "
       pdb=" CA  ASP A 343 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.030 1.33e-02 5.65e+03 5.00e+00
  bond pdb=" N   SER B 316 "
       pdb=" CA  SER B 316 "
    ideal  model  delta    sigma   weight residual
    1.458  1.481 -0.024 1.28e-02 6.10e+03 3.39e+00
  bond pdb=" N   THR R  29 "
       pdb=" CA  THR R  29 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.12e+00
  ... (remaining 12048 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.98: 17672
        0.98 -     1.96: 1165
        1.96 -     2.94: 87
        2.94 -     3.91: 24
        3.91 -     4.89: 10
  Bond angle restraints: 18958
  Sorted by residual:
  angle pdb=" CA  ARG N  98 "
        pdb=" C   ARG N  98 "
        pdb=" O   ARG N  98 "
      ideal   model   delta    sigma   weight residual
     120.70  116.98    3.72 1.08e+00 8.57e-01 1.18e+01
  angle pdb=" N   ILE R 357 "
        pdb=" CA  ILE R 357 "
        pdb=" CB  ILE R 357 "
      ideal   model   delta    sigma   weight residual
     110.45  113.09   -2.64 7.80e-01 1.64e+00 1.15e+01
  angle pdb=" N   VAL R 409 "
        pdb=" CA  VAL R 409 "
        pdb=" C   VAL R 409 "
      ideal   model   delta    sigma   weight residual
     112.96  109.63    3.33 1.00e+00 1.00e+00 1.11e+01
  angle pdb=" C   ILE R 357 "
        pdb=" CA  ILE R 357 "
        pdb=" CB  ILE R 357 "
      ideal   model   delta    sigma   weight residual
     114.00  109.93    4.07 1.31e+00 5.83e-01 9.64e+00
  angle pdb=" N   VAL R 276 "
        pdb=" CA  VAL R 276 "
        pdb=" C   VAL R 276 "
      ideal   model   delta    sigma   weight residual
     112.61  108.18    4.43 1.45e+00 4.76e-01 9.33e+00
  ... (remaining 18953 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.07: 5987
       17.07 -    34.14: 408
       34.14 -    51.21: 91
       51.21 -    68.28: 30
       68.28 -    85.35: 13
  Dihedral angle restraints: 6529
    sinusoidal: 2861
      harmonic: 3668
  Sorted by residual:
  dihedral pdb=" CB  CYS R  62 "
           pdb=" SG  CYS R  62 "
           pdb=" SG  CYS R 104 "
           pdb=" CB  CYS R 104 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -155.05   69.05     1      1.00e+01 1.00e-02 6.17e+01
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -121.96   35.96     1      1.00e+01 1.00e-02 1.83e+01
  dihedral pdb=" CB  CYS R 226 "
           pdb=" SG  CYS R 226 "
           pdb=" SG  CYS R 296 "
           pdb=" CB  CYS R 296 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  123.72  -30.72     1      1.00e+01 1.00e-02 1.35e+01
  ... (remaining 6526 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1108
       0.041 -    0.082: 213
       0.082 -    0.122: 74
       0.122 -    0.163: 2
       0.163 -    0.204: 1
  Chirality restraints: 1398
  Sorted by residual:
  chirality pdb=" CA  ARG N  98 "
            pdb=" N   ARG N  98 "
            pdb=" C   ARG N  98 "
            pdb=" CB  ARG N  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CA  ILE B  81 "
            pdb=" N   ILE B  81 "
            pdb=" C   ILE B  81 "
            pdb=" CB  ILE B  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.12e-01
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.02e-01
  ... (remaining 1395 not shown)

  Planarity restraints: 1992
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.037 5.00e-02 4.00e+02   5.69e-02 5.18e+00
        pdb=" N   PRO B 236 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R 357 "    0.023 5.00e-02 4.00e+02   3.41e-02 1.86e+00
        pdb=" N   PRO R 358 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO R 358 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO R 358 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 276 "   -0.020 5.00e-02 4.00e+02   3.03e-02 1.47e+00
        pdb=" N   PRO R 277 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO R 277 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO R 277 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1989 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 302
        2.21 -     2.80: 13165
        2.80 -     3.40: 22281
        3.40 -     4.00: 31078
        4.00 -     4.60: 47976
  Nonbonded interactions: 114802
  Sorted by model distance:
  nonbonded pdb=" O   LEU R 172 "
            pdb="HD21 ASN R 177 "
     model   vdw
     1.607 2.450
  nonbonded pdb="HD21 ASN R 320 "
            pdb=" O   LEU R 360 "
     model   vdw
     1.700 2.450
  nonbonded pdb=" HZ3 LYS R 334 "
            pdb=" OE1 GLN A 384 "
     model   vdw
     1.707 2.450
  nonbonded pdb=" O   TYR R 178 "
            pdb="HD21 ASN R 182 "
     model   vdw
     1.720 2.450
  nonbonded pdb=" H   LEU R  32 "
            pdb=" OD1 ASP P  15 "
     model   vdw
     1.730 2.450
  ... (remaining 114797 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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 individual isotropic
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:             1.540
  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:             0.070
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.980
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
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      :  0.002   0.052   9203  Z= 0.101
  Angle     :  0.432   4.893  12487  Z= 0.254
  Chirality :  0.037   0.204   1398
  Planarity :  0.003   0.057   1600
  Dihedral  : 12.888  85.355   3254
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.17 (0.25), residues: 1143
  helix:  2.55 (0.25), residues: 458
  sheet:  1.71 (0.35), residues: 206
  loop :  0.25 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 190 
 TYR   0.016   0.001   TYR B  59 
 PHE   0.010   0.001   PHE R 280 
 TRP   0.019   0.001   TRP R 243 
 HIS   0.008   0.001   HIS R 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00181 ( 9197)
  covalent geometry    : angle       0.43073 (12475)
  SS BOND              : bond        0.00116 (    6)
  SS BOND              : angle       0.98694 (   12)
  hydrogen bonds       : bond        0.19863 (  474)
  hydrogen bonds       : angle       6.02083 ( 1305)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   29 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   31 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue THR   35 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue TYR   42 is missing expected H atoms. Skipping.
Residue SER   49 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue THR   51 is missing expected H atoms. Skipping.
Residue THR   58 is missing expected H atoms. Skipping.
Residue LEU   60 is missing expected H atoms. Skipping.
Residue THR   65 is missing expected H atoms. Skipping.
Residue TYR   69 is missing expected H atoms. Skipping.
Residue SER   79 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   83 is missing expected H atoms. Skipping.
Residue SER   84 is missing expected H atoms. Skipping.
Residue TYR   88 is missing expected H atoms. Skipping.
Residue LEU   89 is missing expected H atoms. Skipping.
Residue SER   93 is missing expected H atoms. Skipping.
Residue SER   94 is missing expected H atoms. Skipping.
Residue VAL   95 is missing expected H atoms. Skipping.
Residue VAL  100 is missing expected H atoms. Skipping.
Residue TYR  101 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  109 is missing expected H atoms. Skipping.
Residue LEU  111 is missing expected H atoms. Skipping.
Residue LYS  113 is missing expected H atoms. Skipping.
Residue SER  116 is missing expected H atoms. Skipping.
Residue SER  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  123 is missing expected H atoms. Skipping.
Residue SER  124 is missing expected H atoms. Skipping.
Residue SER  129 is missing expected H atoms. Skipping.
Evaluate side-chains
  126 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  149 THR cc_start: 0.5793 (m) cc_final: 0.5360 (p)
REVERT: R  170 ARG cc_start: 0.6143 (ptp-170) cc_final: 0.5714 (tpp80)
REVERT: R  204 MET cc_start: 0.6242 (mtm) cc_final: 0.5883 (mtm)
REVERT: R  292 GLU cc_start: 0.5484 (tt0) cc_final: 0.5226 (tp30)
REVERT: R  371 MET cc_start: 0.6287 (mmm) cc_final: 0.5671 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.9781
  time to fit residues: 129.5926
Evaluate side-chains
  89 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    0.0270
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    0.9990
   chunk 106 optimal weight:    0.5980
   overall best weight:    0.8442

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

Flipped N/Q/H residues before XYZ refinement:
G  18 GLN
N   5 GLN
N 120 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4634 r_free = 0.4634 target = 0.235580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.180018 restraints weight = 15406.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.4077 rms_B_bonded: 1.92
r_work: 0.3906 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3796 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.1279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   9203  Z= 0.114
  Angle     :  0.472   5.167  12487  Z= 0.260
  Chirality :  0.038   0.136   1398
  Planarity :  0.003   0.056   1600
  Dihedral  :  3.769  18.533   1263
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  :  6.45 %
    Favored  : 92.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.95 (0.25), residues: 1143
  helix:  2.57 (0.24), residues: 465
  sheet:  1.46 (0.34), residues: 208
  loop : -0.10 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 150 
 TYR   0.026   0.001   TYR R 148 
 PHE   0.016   0.001   PHE R 280 
 TRP   0.014   0.001   TRP R 243 
 HIS   0.011   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 9197)
  covalent geometry    : angle       0.47191 (12475)
  SS BOND              : bond        0.00109 (    6)
  SS BOND              : angle       0.71713 (   12)
  hydrogen bonds       : bond        0.05118 (  474)
  hydrogen bonds       : angle       4.52550 ( 1305)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   29 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   31 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue THR   35 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue TYR   42 is missing expected H atoms. Skipping.
Residue SER   49 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue THR   51 is missing expected H atoms. Skipping.
Residue THR   58 is missing expected H atoms. Skipping.
Residue LEU   60 is missing expected H atoms. Skipping.
Residue THR   65 is missing expected H atoms. Skipping.
Residue TYR   69 is missing expected H atoms. Skipping.
Residue SER   79 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   83 is missing expected H atoms. Skipping.
Residue SER   84 is missing expected H atoms. Skipping.
Residue TYR   88 is missing expected H atoms. Skipping.
Residue LEU   89 is missing expected H atoms. Skipping.
Residue SER   93 is missing expected H atoms. Skipping.
Residue SER   94 is missing expected H atoms. Skipping.
Residue VAL   95 is missing expected H atoms. Skipping.
Residue VAL  100 is missing expected H atoms. Skipping.
Residue TYR  101 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  109 is missing expected H atoms. Skipping.
Residue LEU  111 is missing expected H atoms. Skipping.
Residue LYS  113 is missing expected H atoms. Skipping.
Residue SER  116 is missing expected H atoms. Skipping.
Residue SER  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  123 is missing expected H atoms. Skipping.
Residue SER  124 is missing expected H atoms. Skipping.
Residue SER  129 is missing expected H atoms. Skipping.
Evaluate side-chains
  111 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  149 THR cc_start: 0.5809 (m) cc_final: 0.5361 (p)
REVERT: R  170 ARG cc_start: 0.6205 (ptp-170) cc_final: 0.5827 (tpt-90)
REVERT: R  204 MET cc_start: 0.6286 (mtm) cc_final: 0.5910 (mtm)
REVERT: R  292 GLU cc_start: 0.5925 (tt0) cc_final: 0.5340 (tp30)
REVERT: R  294 GLU cc_start: 0.6269 (mp0) cc_final: 0.5963 (mp0)
REVERT: R  299 ARG cc_start: 0.5651 (mtm-85) cc_final: 0.5237 (mmt-90)
REVERT: R  371 MET cc_start: 0.6154 (mmm) cc_final: 0.5508 (mmm)
REVERT: R  414 ARG cc_start: 0.5390 (tpt170) cc_final: 0.4843 (mmm160)
REVERT: A  314 GLU cc_start: 0.6814 (tt0) cc_final: 0.5897 (mp0)
REVERT: B  314 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7444 (ttt180)
  outliers start: 11
  outliers final: 5
  residues processed: 105
  average time/residue: 0.9911
  time to fit residues: 109.4345
Evaluate side-chains
  100 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain G residue   57 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 104 optimal weight:    2.9990
   chunk 92 optimal weight:    4.9990
   chunk 78 optimal weight:    0.1980
   chunk 8 optimal weight:   50.0000
   chunk 101 optimal weight:    3.9990
   chunk 97 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 88 optimal weight:    4.9990
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
P   3 GLN
A 213 GLN
B  54 HIS
B 176 GLN
G  18 GLN
N   5 GLN
N 120 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4591 r_free = 0.4591 target = 0.230454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.171119 restraints weight = 15249.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3990 rms_B_bonded: 2.13
r_work: 0.3841 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3724 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9203  Z= 0.211
  Angle     :  0.608  10.256  12487  Z= 0.328
  Chirality :  0.043   0.161   1398
  Planarity :  0.004   0.061   1600
  Dihedral  :  4.513  21.650   1263
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  :  8.60 %
    Favored  : 89.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.24), residues: 1143
  helix:  2.23 (0.23), residues: 459
  sheet:  0.97 (0.34), residues: 210
  loop : -0.32 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  42 
 TYR   0.025   0.002   TYR R 148 
 PHE   0.029   0.002   PHE B 151 
 TRP   0.021   0.002   TRP R 243 
 HIS   0.016   0.002   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 ( 9197)
  covalent geometry    : angle       0.60811 (12475)
  SS BOND              : bond        0.00119 (    6)
  SS BOND              : angle       0.77061 (   12)
  hydrogen bonds       : bond        0.05598 (  474)
  hydrogen bonds       : angle       4.64570 ( 1305)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   29 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   31 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue THR   35 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue TYR   42 is missing expected H atoms. Skipping.
Residue SER   49 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue THR   51 is missing expected H atoms. Skipping.
Residue THR   58 is missing expected H atoms. Skipping.
Residue LEU   60 is missing expected H atoms. Skipping.
Residue THR   65 is missing expected H atoms. Skipping.
Residue TYR   69 is missing expected H atoms. Skipping.
Residue SER   79 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   83 is missing expected H atoms. Skipping.
Residue SER   84 is missing expected H atoms. Skipping.
Residue TYR   88 is missing expected H atoms. Skipping.
Residue LEU   89 is missing expected H atoms. Skipping.
Residue SER   93 is missing expected H atoms. Skipping.
Residue SER   94 is missing expected H atoms. Skipping.
Residue VAL   95 is missing expected H atoms. Skipping.
Residue VAL  100 is missing expected H atoms. Skipping.
Residue TYR  101 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  109 is missing expected H atoms. Skipping.
Residue LEU  111 is missing expected H atoms. Skipping.
Residue LYS  113 is missing expected H atoms. Skipping.
Residue SER  116 is missing expected H atoms. Skipping.
Residue SER  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  123 is missing expected H atoms. Skipping.
Residue SER  124 is missing expected H atoms. Skipping.
Residue SER  129 is missing expected H atoms. Skipping.
Evaluate side-chains
  116 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  149 THR cc_start: 0.5861 (m) cc_final: 0.5372 (p)
REVERT: R  170 ARG cc_start: 0.6374 (ptp-170) cc_final: 0.5953 (tpt-90)
REVERT: R  204 MET cc_start: 0.6348 (mtm) cc_final: 0.5933 (mtm)
REVERT: R  292 GLU cc_start: 0.5952 (tt0) cc_final: 0.5308 (tp30)
REVERT: R  371 MET cc_start: 0.6206 (mmm) cc_final: 0.5548 (mmm)
REVERT: R  414 ARG cc_start: 0.5426 (tpt170) cc_final: 0.4836 (mmp-170)
REVERT: A  216 LYS cc_start: 0.7942 (mmmm) cc_final: 0.7575 (mtpp)
REVERT: A  314 GLU cc_start: 0.6890 (tt0) cc_final: 0.5925 (mp0)
REVERT: B   23 LYS cc_start: 0.8126 (tttp) cc_final: 0.7827 (tppt)
REVERT: B  195 ASP cc_start: 0.5826 (OUTLIER) cc_final: 0.5585 (p0)
REVERT: B  314 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7665 (ttt180)
REVERT: B  340 ASN cc_start: 0.8462 (OUTLIER) cc_final: 0.7872 (m110)
REVERT: G   21 MET cc_start: 0.5401 (ppp) cc_final: 0.5188 (ppp)
  outliers start: 18
  outliers final: 8
  residues processed: 106
  average time/residue: 0.9614
  time to fit residues: 107.4135
Evaluate side-chains
  105 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  233 MET
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain G residue   57 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 75 optimal weight:    0.0970
   chunk 2 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   chunk 54 optimal weight:   10.0000
   chunk 46 optimal weight:    5.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
B  54 HIS
N 120 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.214739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.140820 restraints weight = 14113.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 2.23
r_work: 0.3489 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3345 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   9203  Z= 0.111
  Angle     :  0.466   5.953  12487  Z= 0.256
  Chirality :  0.038   0.136   1398
  Planarity :  0.003   0.057   1600
  Dihedral  :  4.057  20.004   1263
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 10.00 %
    Favored  : 88.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.63 (0.24), residues: 1143
  helix:  2.54 (0.24), residues: 461
  sheet:  0.85 (0.34), residues: 213
  loop : -0.29 (0.27), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  20 
 TYR   0.022   0.001   TYR R 148 
 PHE   0.016   0.001   PHE B 151 
 TRP   0.016   0.001   TRP A 234 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 9197)
  covalent geometry    : angle       0.46608 (12475)
  SS BOND              : bond        0.00115 (    6)
  SS BOND              : angle       0.43165 (   12)
  hydrogen bonds       : bond        0.04414 (  474)
  hydrogen bonds       : angle       4.28699 ( 1305)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   29 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   31 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue THR   35 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue TYR   42 is missing expected H atoms. Skipping.
Residue SER   49 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue THR   51 is missing expected H atoms. Skipping.
Residue THR   58 is missing expected H atoms. Skipping.
Residue LEU   60 is missing expected H atoms. Skipping.
Residue THR   65 is missing expected H atoms. Skipping.
Residue TYR   69 is missing expected H atoms. Skipping.
Residue SER   79 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   83 is missing expected H atoms. Skipping.
Residue SER   84 is missing expected H atoms. Skipping.
Residue TYR   88 is missing expected H atoms. Skipping.
Residue LEU   89 is missing expected H atoms. Skipping.
Residue SER   93 is missing expected H atoms. Skipping.
Residue SER   94 is missing expected H atoms. Skipping.
Residue VAL   95 is missing expected H atoms. Skipping.
Residue VAL  100 is missing expected H atoms. Skipping.
Residue TYR  101 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  109 is missing expected H atoms. Skipping.
Residue LEU  111 is missing expected H atoms. Skipping.
Residue LYS  113 is missing expected H atoms. Skipping.
Residue SER  116 is missing expected H atoms. Skipping.
Residue SER  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  123 is missing expected H atoms. Skipping.
Residue SER  124 is missing expected H atoms. Skipping.
Residue SER  129 is missing expected H atoms. Skipping.
Evaluate side-chains
  108 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  149 THR cc_start: 0.5303 (m) cc_final: 0.4809 (p)
REVERT: R  170 ARG cc_start: 0.6221 (ptp-170) cc_final: 0.5707 (tpt-90)
REVERT: R  204 MET cc_start: 0.6285 (mtm) cc_final: 0.5874 (mtm)
REVERT: R  292 GLU cc_start: 0.6147 (tt0) cc_final: 0.5445 (tp30)
REVERT: R  371 MET cc_start: 0.5940 (mmm) cc_final: 0.5312 (mmm)
REVERT: R  414 ARG cc_start: 0.5587 (tpt170) cc_final: 0.4760 (mmp-170)
REVERT: A  216 LYS cc_start: 0.7878 (mmmm) cc_final: 0.7525 (mtpp)
REVERT: A  314 GLU cc_start: 0.6824 (tt0) cc_final: 0.5699 (mp0)
REVERT: B   23 LYS cc_start: 0.7781 (tttp) cc_final: 0.7487 (tppt)
REVERT: B  195 ASP cc_start: 0.5566 (OUTLIER) cc_final: 0.5321 (p0)
REVERT: B  314 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7482 (ttt180)
REVERT: B  340 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.7883 (m110)
  outliers start: 14
  outliers final: 7
  residues processed: 101
  average time/residue: 0.9616
  time to fit residues: 102.6426
Evaluate side-chains
  103 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain G residue   57 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 104 optimal weight:    0.9980
   chunk 74 optimal weight:    4.9990
   chunk 26 optimal weight:   20.0000
   chunk 109 optimal weight:    0.8980
   chunk 82 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 112 optimal weight:    0.1980
   chunk 81 optimal weight:    0.7980
   chunk 94 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 89 optimal weight:    0.0370
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
N 120 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.216184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.142871 restraints weight = 14211.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.3663 rms_B_bonded: 2.22
r_work: 0.3513 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3370 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.2063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9203  Z= 0.089
  Angle     :  0.425   4.453  12487  Z= 0.234
  Chirality :  0.037   0.130   1398
  Planarity :  0.003   0.053   1600
  Dihedral  :  3.781  18.348   1263
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 10.75 %
    Favored  : 87.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.84 (0.24), residues: 1143
  helix:  2.80 (0.24), residues: 461
  sheet:  0.92 (0.34), residues: 210
  loop : -0.25 (0.27), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  20 
 TYR   0.022   0.001   TYR R 148 
 PHE   0.015   0.001   PHE R 280 
 TRP   0.015   0.001   TRP A 234 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00184 ( 9197)
  covalent geometry    : angle       0.42509 (12475)
  SS BOND              : bond        0.00110 (    6)
  SS BOND              : angle       0.32690 (   12)
  hydrogen bonds       : bond        0.03893 (  474)
  hydrogen bonds       : angle       4.06112 ( 1305)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   29 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   31 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue THR   35 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue TYR   42 is missing expected H atoms. Skipping.
Residue SER   49 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue THR   51 is missing expected H atoms. Skipping.
Residue THR   58 is missing expected H atoms. Skipping.
Residue LEU   60 is missing expected H atoms. Skipping.
Residue THR   65 is missing expected H atoms. Skipping.
Residue TYR   69 is missing expected H atoms. Skipping.
Residue SER   79 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   83 is missing expected H atoms. Skipping.
Residue SER   84 is missing expected H atoms. Skipping.
Residue TYR   88 is missing expected H atoms. Skipping.
Residue LEU   89 is missing expected H atoms. Skipping.
Residue SER   93 is missing expected H atoms. Skipping.
Residue SER   94 is missing expected H atoms. Skipping.
Residue VAL   95 is missing expected H atoms. Skipping.
Residue VAL  100 is missing expected H atoms. Skipping.
Residue TYR  101 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  109 is missing expected H atoms. Skipping.
Residue LEU  111 is missing expected H atoms. Skipping.
Residue LYS  113 is missing expected H atoms. Skipping.
Residue SER  116 is missing expected H atoms. Skipping.
Residue SER  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  123 is missing expected H atoms. Skipping.
Residue SER  124 is missing expected H atoms. Skipping.
Residue SER  129 is missing expected H atoms. Skipping.
Evaluate side-chains
  110 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  149 THR cc_start: 0.5382 (m) cc_final: 0.4911 (p)
REVERT: R  170 ARG cc_start: 0.6250 (ptp-170) cc_final: 0.5674 (tpt-90)
REVERT: R  204 MET cc_start: 0.6274 (mtm) cc_final: 0.5514 (mmm)
REVERT: R  292 GLU cc_start: 0.6184 (tt0) cc_final: 0.5445 (tp30)
REVERT: R  371 MET cc_start: 0.5963 (mmm) cc_final: 0.5322 (mmm)
REVERT: R  414 ARG cc_start: 0.5594 (tpt170) cc_final: 0.4774 (mmp-170)
REVERT: A  314 GLU cc_start: 0.6817 (tt0) cc_final: 0.5672 (mp0)
REVERT: B  195 ASP cc_start: 0.5535 (OUTLIER) cc_final: 0.5276 (p0)
REVERT: B  314 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7426 (ttt180)
REVERT: G   21 MET cc_start: 0.5046 (ppp) cc_final: 0.4780 (ppp)
  outliers start: 14
  outliers final: 7
  residues processed: 104
  average time/residue: 1.0699
  time to fit residues: 117.1953
Evaluate side-chains
  98 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 70 optimal weight:    0.6980
   chunk 64 optimal weight:    3.9990
   chunk 86 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 100 optimal weight:    0.7980
   chunk 66 optimal weight:    5.9990
   chunk 83 optimal weight:    4.9990
   chunk 11 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 120 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.213967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.139823 restraints weight = 14217.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.3627 rms_B_bonded: 2.23
r_work: 0.3475 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3329 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.2239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9203  Z= 0.131
  Angle     :  0.486   7.559  12487  Z= 0.263
  Chirality :  0.039   0.141   1398
  Planarity :  0.003   0.054   1600
  Dihedral  :  4.059  20.299   1263
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 10.54 %
    Favored  : 87.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.71 (0.24), residues: 1143
  helix:  2.70 (0.24), residues: 461
  sheet:  0.82 (0.34), residues: 211
  loop : -0.31 (0.27), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  20 
 TYR   0.021   0.001   TYR R 148 
 PHE   0.020   0.002   PHE B 151 
 TRP   0.016   0.001   TRP A 234 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9197)
  covalent geometry    : angle       0.48569 (12475)
  SS BOND              : bond        0.00084 (    6)
  SS BOND              : angle       0.45916 (   12)
  hydrogen bonds       : bond        0.04384 (  474)
  hydrogen bonds       : angle       4.20596 ( 1305)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   29 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   31 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue THR   35 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue TYR   42 is missing expected H atoms. Skipping.
Residue SER   49 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue THR   51 is missing expected H atoms. Skipping.
Residue THR   58 is missing expected H atoms. Skipping.
Residue LEU   60 is missing expected H atoms. Skipping.
Residue THR   65 is missing expected H atoms. Skipping.
Residue TYR   69 is missing expected H atoms. Skipping.
Residue SER   79 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   83 is missing expected H atoms. Skipping.
Residue SER   84 is missing expected H atoms. Skipping.
Residue TYR   88 is missing expected H atoms. Skipping.
Residue LEU   89 is missing expected H atoms. Skipping.
Residue SER   93 is missing expected H atoms. Skipping.
Residue SER   94 is missing expected H atoms. Skipping.
Residue VAL   95 is missing expected H atoms. Skipping.
Residue VAL  100 is missing expected H atoms. Skipping.
Residue TYR  101 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  109 is missing expected H atoms. Skipping.
Residue LEU  111 is missing expected H atoms. Skipping.
Residue LYS  113 is missing expected H atoms. Skipping.
Residue SER  116 is missing expected H atoms. Skipping.
Residue SER  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  123 is missing expected H atoms. Skipping.
Residue SER  124 is missing expected H atoms. Skipping.
Residue SER  129 is missing expected H atoms. Skipping.
Evaluate side-chains
  109 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  170 ARG cc_start: 0.6279 (ptp-170) cc_final: 0.5711 (tpt-90)
REVERT: R  371 MET cc_start: 0.5917 (mmm) cc_final: 0.5225 (mmm)
REVERT: R  414 ARG cc_start: 0.5736 (tpt170) cc_final: 0.4935 (mmp-170)
REVERT: A  314 GLU cc_start: 0.6866 (tt0) cc_final: 0.5725 (mp0)
REVERT: B  195 ASP cc_start: 0.5527 (OUTLIER) cc_final: 0.5285 (p0)
REVERT: B  314 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7502 (ttt180)
REVERT: B  340 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.7985 (m-40)
REVERT: G   21 MET cc_start: 0.4882 (ppp) cc_final: 0.4560 (ppp)
  outliers start: 19
  outliers final: 11
  residues processed: 100
  average time/residue: 1.0269
  time to fit residues: 108.3201
Evaluate side-chains
  102 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 81 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 38 optimal weight:    9.9990
   chunk 77 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 66 optimal weight:    4.9990
   chunk 107 optimal weight:    4.9990
   chunk 111 optimal weight:    2.9990
   chunk 99 optimal weight:    0.8980
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 120 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.211117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.136535 restraints weight = 14041.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3591 rms_B_bonded: 2.22
r_work: 0.3437 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3292 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.2488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   9203  Z= 0.219
  Angle     :  0.614  10.841  12487  Z= 0.329
  Chirality :  0.043   0.158   1398
  Planarity :  0.004   0.058   1600
  Dihedral  :  4.534  21.684   1263
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 10.97 %
    Favored  : 86.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.24), residues: 1143
  helix:  2.28 (0.23), residues: 461
  sheet:  0.60 (0.34), residues: 212
  loop : -0.48 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  42 
 TYR   0.021   0.002   TYR R 148 
 PHE   0.028   0.002   PHE B 151 
 TRP   0.019   0.002   TRP A 234 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 9197)
  covalent geometry    : angle       0.61403 (12475)
  SS BOND              : bond        0.00170 (    6)
  SS BOND              : angle       0.55685 (   12)
  hydrogen bonds       : bond        0.05324 (  474)
  hydrogen bonds       : angle       4.49887 ( 1305)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   29 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   31 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue THR   35 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue TYR   42 is missing expected H atoms. Skipping.
Residue SER   49 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue THR   51 is missing expected H atoms. Skipping.
Residue THR   58 is missing expected H atoms. Skipping.
Residue LEU   60 is missing expected H atoms. Skipping.
Residue THR   65 is missing expected H atoms. Skipping.
Residue TYR   69 is missing expected H atoms. Skipping.
Residue SER   79 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   83 is missing expected H atoms. Skipping.
Residue SER   84 is missing expected H atoms. Skipping.
Residue TYR   88 is missing expected H atoms. Skipping.
Residue LEU   89 is missing expected H atoms. Skipping.
Residue SER   93 is missing expected H atoms. Skipping.
Residue SER   94 is missing expected H atoms. Skipping.
Residue VAL   95 is missing expected H atoms. Skipping.
Residue VAL  100 is missing expected H atoms. Skipping.
Residue TYR  101 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  109 is missing expected H atoms. Skipping.
Residue LEU  111 is missing expected H atoms. Skipping.
Residue LYS  113 is missing expected H atoms. Skipping.
Residue SER  116 is missing expected H atoms. Skipping.
Residue SER  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  123 is missing expected H atoms. Skipping.
Residue SER  124 is missing expected H atoms. Skipping.
Residue SER  129 is missing expected H atoms. Skipping.
Evaluate side-chains
  110 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  170 ARG cc_start: 0.6295 (ptp-170) cc_final: 0.5755 (tpt-90)
REVERT: R  414 ARG cc_start: 0.5823 (tpt170) cc_final: 0.5111 (mmp-170)
REVERT: A  216 LYS cc_start: 0.7864 (mmmm) cc_final: 0.7540 (mtpp)
REVERT: A  314 GLU cc_start: 0.6875 (tt0) cc_final: 0.5742 (mp0)
REVERT: B  195 ASP cc_start: 0.5551 (OUTLIER) cc_final: 0.5299 (p0)
REVERT: B  314 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7654 (ttt180)
REVERT: B  340 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.7986 (m-40)
  outliers start: 19
  outliers final: 11
  residues processed: 102
  average time/residue: 1.0253
  time to fit residues: 110.2920
Evaluate side-chains
  100 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  233 MET
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 6 optimal weight:   20.0000
   chunk 28 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 107 optimal weight:    3.9990
   chunk 0 optimal weight:   50.0000
   chunk 72 optimal weight:    0.0870
   chunk 90 optimal weight:    0.8980
   chunk 111 optimal weight:    0.0270
   chunk 64 optimal weight:    8.9990
   chunk 46 optimal weight:    3.9990
   overall best weight:    0.8020

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 120 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.214308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.140832 restraints weight = 14167.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 2.23
r_work: 0.3478 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3335 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.2484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9203  Z= 0.102
  Angle     :  0.452   5.078  12487  Z= 0.249
  Chirality :  0.038   0.137   1398
  Planarity :  0.003   0.056   1600
  Dihedral  :  3.995  19.853   1263
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 12.26 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.60 (0.25), residues: 1143
  helix:  2.69 (0.24), residues: 461
  sheet:  0.62 (0.34), residues: 214
  loop : -0.38 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 314 
 TYR   0.019   0.001   TYR R 148 
 PHE   0.016   0.001   PHE R 280 
 TRP   0.016   0.001   TRP A 234 
 HIS   0.008   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 9197)
  covalent geometry    : angle       0.45247 (12475)
  SS BOND              : bond        0.00134 (    6)
  SS BOND              : angle       0.36134 (   12)
  hydrogen bonds       : bond        0.04108 (  474)
  hydrogen bonds       : angle       4.13560 ( 1305)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   29 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   31 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue THR   35 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue TYR   42 is missing expected H atoms. Skipping.
Residue SER   49 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue THR   51 is missing expected H atoms. Skipping.
Residue THR   58 is missing expected H atoms. Skipping.
Residue LEU   60 is missing expected H atoms. Skipping.
Residue THR   65 is missing expected H atoms. Skipping.
Residue TYR   69 is missing expected H atoms. Skipping.
Residue SER   79 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   83 is missing expected H atoms. Skipping.
Residue SER   84 is missing expected H atoms. Skipping.
Residue TYR   88 is missing expected H atoms. Skipping.
Residue LEU   89 is missing expected H atoms. Skipping.
Residue SER   93 is missing expected H atoms. Skipping.
Residue SER   94 is missing expected H atoms. Skipping.
Residue VAL   95 is missing expected H atoms. Skipping.
Residue VAL  100 is missing expected H atoms. Skipping.
Residue TYR  101 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  109 is missing expected H atoms. Skipping.
Residue LEU  111 is missing expected H atoms. Skipping.
Residue LYS  113 is missing expected H atoms. Skipping.
Residue SER  116 is missing expected H atoms. Skipping.
Residue SER  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  123 is missing expected H atoms. Skipping.
Residue SER  124 is missing expected H atoms. Skipping.
Residue SER  129 is missing expected H atoms. Skipping.
Evaluate side-chains
  100 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  170 ARG cc_start: 0.6296 (ptp-170) cc_final: 0.5662 (tpt-90)
REVERT: R  292 GLU cc_start: 0.6262 (tt0) cc_final: 0.5612 (tp30)
REVERT: R  408 GLU cc_start: 0.6765 (mt-10) cc_final: 0.6041 (mt-10)
REVERT: R  414 ARG cc_start: 0.5808 (tpt170) cc_final: 0.5106 (mmp-170)
REVERT: A  314 GLU cc_start: 0.6874 (tt0) cc_final: 0.5729 (mp0)
REVERT: B  195 ASP cc_start: 0.5536 (OUTLIER) cc_final: 0.5294 (p0)
REVERT: B  314 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7466 (ttt180)
REVERT: B  340 ASN cc_start: 0.8495 (OUTLIER) cc_final: 0.7942 (m-40)
REVERT: G   21 MET cc_start: 0.4923 (ppp) cc_final: 0.4582 (ppp)
  outliers start: 10
  outliers final: 5
  residues processed: 97
  average time/residue: 1.0087
  time to fit residues: 103.2884
Evaluate side-chains
  95 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 33 optimal weight:   10.0000
   chunk 60 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 23 optimal weight:    5.9990
   chunk 81 optimal weight:    6.9990
   chunk 111 optimal weight:    0.9980
   chunk 107 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 120 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.212919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.138946 restraints weight = 14051.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 2.21
r_work: 0.3466 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3324 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.2585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9203  Z= 0.138
  Angle     :  0.504   8.040  12487  Z= 0.274
  Chirality :  0.039   0.140   1398
  Planarity :  0.003   0.056   1600
  Dihedral  :  4.172  20.822   1263
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 11.94 %
    Favored  : 86.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.55 (0.24), residues: 1143
  helix:  2.60 (0.24), residues: 461
  sheet:  0.68 (0.34), residues: 211
  loop : -0.42 (0.27), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  42 
 TYR   0.020   0.002   TYR R 148 
 PHE   0.020   0.002   PHE B 151 
 TRP   0.018   0.002   TRP A 234 
 HIS   0.013   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 9197)
  covalent geometry    : angle       0.50399 (12475)
  SS BOND              : bond        0.00096 (    6)
  SS BOND              : angle       0.57699 (   12)
  hydrogen bonds       : bond        0.04478 (  474)
  hydrogen bonds       : angle       4.23714 ( 1305)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   29 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   31 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue THR   35 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue TYR   42 is missing expected H atoms. Skipping.
Residue SER   49 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue THR   51 is missing expected H atoms. Skipping.
Residue THR   58 is missing expected H atoms. Skipping.
Residue LEU   60 is missing expected H atoms. Skipping.
Residue THR   65 is missing expected H atoms. Skipping.
Residue TYR   69 is missing expected H atoms. Skipping.
Residue SER   79 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   83 is missing expected H atoms. Skipping.
Residue SER   84 is missing expected H atoms. Skipping.
Residue TYR   88 is missing expected H atoms. Skipping.
Residue LEU   89 is missing expected H atoms. Skipping.
Residue SER   93 is missing expected H atoms. Skipping.
Residue SER   94 is missing expected H atoms. Skipping.
Residue VAL   95 is missing expected H atoms. Skipping.
Residue VAL  100 is missing expected H atoms. Skipping.
Residue TYR  101 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  109 is missing expected H atoms. Skipping.
Residue LEU  111 is missing expected H atoms. Skipping.
Residue LYS  113 is missing expected H atoms. Skipping.
Residue SER  116 is missing expected H atoms. Skipping.
Residue SER  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  123 is missing expected H atoms. Skipping.
Residue SER  124 is missing expected H atoms. Skipping.
Residue SER  129 is missing expected H atoms. Skipping.
Evaluate side-chains
  101 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  170 ARG cc_start: 0.6285 (ptp-170) cc_final: 0.5765 (tpt-90)
REVERT: R  408 GLU cc_start: 0.6807 (mt-10) cc_final: 0.6121 (mt-10)
REVERT: R  414 ARG cc_start: 0.5850 (tpt170) cc_final: 0.5130 (mmp-170)
REVERT: A  314 GLU cc_start: 0.6844 (tt0) cc_final: 0.5712 (mp0)
REVERT: B  195 ASP cc_start: 0.5504 (OUTLIER) cc_final: 0.5266 (p0)
REVERT: B  314 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7495 (ttt180)
REVERT: B  340 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.7938 (m-40)
REVERT: G   21 MET cc_start: 0.4876 (ppp) cc_final: 0.4534 (ppp)
  outliers start: 12
  outliers final: 8
  residues processed: 96
  average time/residue: 1.0094
  time to fit residues: 102.3766
Evaluate side-chains
  97 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 97 optimal weight:    6.9990
   chunk 44 optimal weight:    0.6980
   chunk 70 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 94 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 109 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0060
   chunk 19 optimal weight:    5.9990
   overall best weight:    1.0798

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 120 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.213895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.144094 restraints weight = 14250.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 2.79
r_work: 0.3447 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3303 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.2602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9203  Z= 0.118
  Angle     :  0.478   6.511  12487  Z= 0.260
  Chirality :  0.039   0.137   1398
  Planarity :  0.003   0.056   1600
  Dihedral  :  4.052  20.079   1263
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 11.94 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.62 (0.25), residues: 1143
  helix:  2.69 (0.24), residues: 461
  sheet:  0.65 (0.34), residues: 213
  loop : -0.38 (0.27), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  42 
 TYR   0.019   0.001   TYR R 148 
 PHE   0.019   0.001   PHE B 151 
 TRP   0.016   0.001   TRP A 234 
 HIS   0.011   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 9197)
  covalent geometry    : angle       0.47745 (12475)
  SS BOND              : bond        0.00221 (    6)
  SS BOND              : angle       0.63954 (   12)
  hydrogen bonds       : bond        0.04208 (  474)
  hydrogen bonds       : angle       4.15518 ( 1305)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   29 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   31 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue THR   35 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue TYR   42 is missing expected H atoms. Skipping.
Residue SER   49 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue THR   51 is missing expected H atoms. Skipping.
Residue THR   58 is missing expected H atoms. Skipping.
Residue LEU   60 is missing expected H atoms. Skipping.
Residue THR   65 is missing expected H atoms. Skipping.
Residue TYR   69 is missing expected H atoms. Skipping.
Residue SER   79 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   83 is missing expected H atoms. Skipping.
Residue SER   84 is missing expected H atoms. Skipping.
Residue TYR   88 is missing expected H atoms. Skipping.
Residue LEU   89 is missing expected H atoms. Skipping.
Residue SER   93 is missing expected H atoms. Skipping.
Residue SER   94 is missing expected H atoms. Skipping.
Residue VAL   95 is missing expected H atoms. Skipping.
Residue VAL  100 is missing expected H atoms. Skipping.
Residue TYR  101 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  109 is missing expected H atoms. Skipping.
Residue LEU  111 is missing expected H atoms. Skipping.
Residue LYS  113 is missing expected H atoms. Skipping.
Residue SER  116 is missing expected H atoms. Skipping.
Residue SER  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  123 is missing expected H atoms. Skipping.
Residue SER  124 is missing expected H atoms. Skipping.
Residue SER  129 is missing expected H atoms. Skipping.
Evaluate side-chains
  99 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  170 ARG cc_start: 0.6254 (ptp-170) cc_final: 0.5606 (tpt-90)
REVERT: R  408 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6229 (mt-10)
REVERT: R  414 ARG cc_start: 0.5855 (tpt170) cc_final: 0.5165 (mmp-170)
REVERT: B  195 ASP cc_start: 0.5356 (OUTLIER) cc_final: 0.5118 (p0)
REVERT: B  314 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7421 (ttt180)
REVERT: B  340 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.7929 (m-40)
REVERT: G   21 MET cc_start: 0.4646 (ppp) cc_final: 0.4311 (ppp)
  outliers start: 13
  outliers final: 8
  residues processed: 94
  average time/residue: 1.0053
  time to fit residues: 99.7853
Evaluate side-chains
  97 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 106 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 84 optimal weight:    4.9990
   chunk 71 optimal weight:    3.9990
   chunk 108 optimal weight:    0.1980
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 120 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.212407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.138300 restraints weight = 14112.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 2.21
r_work: 0.3458 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3318 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.2721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9203  Z= 0.152
  Angle     :  0.535   9.126  12487  Z= 0.288
  Chirality :  0.040   0.140   1398
  Planarity :  0.004   0.057   1600
  Dihedral  :  4.282  21.190   1263
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 12.26 %
    Favored  : 86.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.45 (0.24), residues: 1143
  helix:  2.52 (0.24), residues: 461
  sheet:  0.63 (0.34), residues: 211
  loop : -0.46 (0.27), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  42 
 TYR   0.020   0.002   TYR R 148 
 PHE   0.023   0.002   PHE B 151 
 TRP   0.018   0.002   TRP A 234 
 HIS   0.013   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 9197)
  covalent geometry    : angle       0.53462 (12475)
  SS BOND              : bond        0.00158 (    6)
  SS BOND              : angle       0.68418 (   12)
  hydrogen bonds       : bond        0.04632 (  474)
  hydrogen bonds       : angle       4.29683 ( 1305)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5963.98 seconds
wall clock time: 101 minutes 49.32 seconds (6109.32 seconds total)