Starting phenix.real_space_refine
on Fri Aug 22 17:00:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gef_29968/08_2025/8gef_29968.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gef_29968/08_2025/8gef_29968.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gef_29968/08_2025/8gef_29968.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gef_29968/08_2025/8gef_29968.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gef_29968/08_2025/8gef_29968.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gef_29968/08_2025/8gef_29968.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.025
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: 4
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    4014      2.51       5
     N    1095      2.21       5
     O    1083      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6216
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 1835
          Classifications: {'peptide': 281}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 138}
          Link IDs: {'PTRANS': 6, 'TRANS': 274}
          Chain breaks: 7
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 500
          Unresolved non-hydrogen angles: 616
          Unresolved non-hydrogen dihedrals: 394
          Unresolved non-hydrogen chiralities: 32
          Planarities with less than four sites: {'GLN:plan1': 12, 'ARG:plan': 17, 'ASN:plan1': 8, 'GLU:plan': 21, 'ASP:plan': 16, 'TYR:plan': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 309
    Chain: "B"
      Number of atoms: 2131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2131
          Classifications: {'peptide': 329}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 124}
          Link IDs: {'PTRANS': 5, 'TRANS': 323}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 396
          Unresolved non-hydrogen angles: 498
          Unresolved non-hydrogen dihedrals: 304
          Unresolved non-hydrogen chiralities: 27
          Planarities with less than four sites: {'ARG:plan': 13, 'GLN:plan1': 8, 'GLU:plan': 6, 'ASN:plan1': 11, 'ASP:plan': 26, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN%COO:plan1': 1}
          Unresolved non-hydrogen planarities: 260
    Chain: "G"
      Number of atoms: 287
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 287
          Classifications: {'peptide': 50}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 4, 'TRANS': 45}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 106
          Unresolved non-hydrogen angles: 128
          Unresolved non-hydrogen dihedrals: 87
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 5, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 54
    Chain: "R"
      Number of atoms: 1948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 1948
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 99}
          Link IDs: {'PTRANS': 7, 'TRANS': 273}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 319
          Unresolved non-hydrogen angles: 403
          Unresolved non-hydrogen dihedrals: 253
          Unresolved non-hydrogen chiralities: 40
          Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 4, 'ASN:plan1': 5, 'GLU:plan': 7, 'ARG:plan': 4, 'GLN:plan1': 7, 'ASP:plan': 5, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 144
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.71, per 1000 atoms: 0.28
  Number of scatterers: 6216
  At special positions: 0
  Unit cell: (67.84, 97.52, 130.38, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      24     16.00
     O    1083      8.00
     N    1095      7.00
     C    4014      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " 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: 0.67
  Conformation dependent library (CDL) restraints added in 526.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1786

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 8 sheets defined
      50.5% alpha, 14.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 40
    Processing helix  chain 'A' and resid 52 through 61
      removed outlier: 3.796A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 108
    Processing helix  chain 'A' and resid 129 through 135
    Processing helix  chain 'A' and resid 159 through 165
      removed outlier: 3.718A  pdb=" N   TYR A 163 " --> pdb=" O   VAL A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 199
    Processing helix  chain 'A' and resid 234 through 238
    Processing helix  chain 'A' and resid 251 through 254
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 307 through 312
    Processing helix  chain 'A' and resid 313 through 316
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.504A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   GLY A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 390
    Processing helix  chain 'A' and resid 391 through 393
      No H-bonds generated for 'chain 'A' and resid 391 through 393'
    Processing helix  chain 'B' and resid 8 through 25
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.521A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 14 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'R' and resid 32 through 61
      removed outlier: 3.957A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 68 through 97
      removed outlier: 3.809A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
    Processing helix  chain 'R' and resid 137 through 145
      removed outlier: 4.083A  pdb=" N   GLN R 142 " --> pdb=" O   PRO R 138 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   SER R 143 " --> pdb=" O   PHE R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 4.456A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
    Processing helix  chain 'R' and resid 172 through 175
    Processing helix  chain 'R' and resid 181 through 187
    Processing helix  chain 'R' and resid 198 through 208
    Processing helix  chain 'R' and resid 208 through 237
    Processing helix  chain 'R' and resid 270 through 299
      removed outlier: 3.670A  pdb=" N   THR R 274 " --> pdb=" O   LYS R 270 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 4.326A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
    Processing helix  chain 'R' and resid 317 through 327
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 340
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213
      removed outlier: 6.735A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.566A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.312A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 7.794A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 8.116A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.910A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.061A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.678A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.062A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105
      removed outlier: 4.037A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.635A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 190 through 192
      removed outlier: 3.710A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.624A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277
      removed outlier: 4.088A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 5.794A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.005A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    385 hydrogen bonds defined for protein.
    1110 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.98

  Time building geometry restraints manager: 0.87 seconds

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

  Histogram of bond lengths:
        1.22 -     1.46: 3717
        1.46 -     1.71: 2589
        1.71 -     1.96: 34
        1.96 -     2.20: 0
        2.20 -     2.45: 1
  Bond restraints: 6341
  Sorted by residual:
  bond pdb=" C   PRO A 328 "
       pdb=" N   GLU A 330 "
    ideal  model  delta    sigma   weight residual
    1.332  2.449 -1.116 1.40e-02 5.10e+03 6.36e+03
  bond pdb=" C   PRO A 332 "
       pdb=" N   ARG A 333 "
    ideal  model  delta    sigma   weight residual
    1.335  1.247  0.088 1.31e-02 5.83e+03 4.47e+01
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.602 -0.079 2.00e-02 2.50e+03 1.56e+01
  bond pdb=" CA  LEU B 168 "
       pdb=" C   LEU B 168 "
    ideal  model  delta    sigma   weight residual
    1.522  1.480  0.042 1.20e-02 6.94e+03 1.25e+01
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.448 -0.051 2.00e-02 2.50e+03 6.56e+00
  ... (remaining 6336 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     9.76: 8715
        9.76 -    19.51: 0
       19.51 -    29.27: 0
       29.27 -    39.03: 1
       39.03 -    48.79: 2
  Bond angle restraints: 8718
  Sorted by residual:
  angle pdb=" O   PRO A 328 "
        pdb=" C   PRO A 328 "
        pdb=" N   GLU A 330 "
      ideal   model   delta    sigma   weight residual
     122.64   84.01   38.63 1.35e+00 5.49e-01 8.19e+02
  angle pdb=" C   PRO A 328 "
        pdb=" N   GLU A 330 "
        pdb=" CA  GLU A 330 "
      ideal   model   delta    sigma   weight residual
     121.54  170.33  -48.79 1.91e+00 2.74e-01 6.52e+02
  angle pdb=" CA  PRO A 328 "
        pdb=" C   PRO A 328 "
        pdb=" N   GLU A 330 "
      ideal   model   delta    sigma   weight residual
     116.70  157.23  -40.53 2.07e+00 2.33e-01 3.83e+02
  angle pdb=" O   PRO A 332 "
        pdb=" C   PRO A 332 "
        pdb=" N   ARG A 333 "
      ideal   model   delta    sigma   weight residual
     122.23  115.52    6.71 1.20e+00 6.94e-01 3.13e+01
  angle pdb=" N   GLU A 327 "
        pdb=" CA  GLU A 327 "
        pdb=" C   GLU A 327 "
      ideal   model   delta    sigma   weight residual
     109.58  117.63   -8.05 1.63e+00 3.76e-01 2.44e+01
  ... (remaining 8713 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.39: 3374
       20.39 -    40.78: 210
       40.78 -    61.17: 18
       61.17 -    81.56: 1
       81.56 -   101.95: 3
  Dihedral angle restraints: 3606
    sinusoidal: 866
      harmonic: 2740
  Sorted by residual:
  dihedral pdb=" CA  PRO A 328 "
           pdb=" C   PRO A 328 "
           pdb=" N   GLU A 330 "
           pdb=" CA  GLU A 330 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -78.05 -101.95     0      5.00e+00 4.00e-02 4.16e+02
  dihedral pdb=" CAE G1I R 501 "
           pdb=" CAG G1I R 501 "
           pdb=" CAH G1I R 501 "
           pdb=" CAI G1I R 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      47.24  -48.83   96.07     1      3.00e+01 1.11e-03 1.18e+01
  dihedral pdb=" CA  MET R 171 "
           pdb=" C   MET R 171 "
           pdb=" N   HIS R 172 "
           pdb=" CA  HIS R 172 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.31  -16.69     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 3603 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 758
       0.034 -    0.068: 218
       0.068 -    0.101: 63
       0.101 -    0.135: 32
       0.135 -    0.169: 4
  Chirality restraints: 1075
  Sorted by residual:
  chirality pdb=" CA  CYS B 166 "
            pdb=" N   CYS B 166 "
            pdb=" C   CYS B 166 "
            pdb=" CB  CYS B 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.14e-01
  chirality pdb=" CB  VAL R 292 "
            pdb=" CA  VAL R 292 "
            pdb=" CG1 VAL R 292 "
            pdb=" CG2 VAL R 292 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.86e-01
  chirality pdb=" CB  THR R 118 "
            pdb=" CA  THR R 118 "
            pdb=" OG1 THR R 118 "
            pdb=" CG2 THR R 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.14 2.00e-01 2.50e+01 5.11e-01
  ... (remaining 1072 not shown)

  Planarity restraints: 1111
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 328 "    0.031 2.00e-02 2.50e+03   3.65e-02 1.33e+01
        pdb=" C   PRO A 328 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   PRO A 328 "    0.014 2.00e-02 2.50e+03
        pdb=" N   GLU A 330 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 297 "   -0.006 2.00e-02 2.50e+03   8.22e-03 1.69e+00
        pdb=" CG  TRP B 297 "    0.021 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 297 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 297 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 297 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 297 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 297 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 297 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 297 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 297 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 326 "   -0.006 2.00e-02 2.50e+03   1.14e-02 1.31e+00
        pdb=" C   PRO A 326 "    0.020 2.00e-02 2.50e+03
        pdb=" O   PRO A 326 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   GLU A 327 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1108 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2027
        2.82 -     3.34: 5939
        3.34 -     3.86: 10232
        3.86 -     4.38: 10224
        4.38 -     4.90: 18745
  Nonbonded interactions: 47167
  Sorted by model distance:
  nonbonded pdb=" O   LYS B  57 "
            pdb=" OG  SER B  74 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" NH1 ARG A 385 "
            pdb=" OE1 GLN R 229 "
     model   vdw
     2.322 3.120
  nonbonded pdb=" O   HIS B  54 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" O   ASP B 186 "
            pdb=" N   CYS B 204 "
     model   vdw
     2.336 3.120
  nonbonded pdb=" OH  TYR R 209 "
            pdb=" O   PHE R 290 "
     model   vdw
     2.356 3.040
  ... (remaining 47162 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.060
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
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      :  0.014   1.116   6342  Z= 1.025
  Angle     :  0.957  48.785   8720  Z= 0.558
  Chirality :  0.040   0.169   1075
  Planarity :  0.003   0.037   1111
  Dihedral  : 13.648 101.948   1817
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 17.02 %
    Favored  : 81.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.13 (0.29), residues: 911
  helix:  3.07 (0.25), residues: 415
  sheet:  0.62 (0.43), residues: 160
  loop : -0.34 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  49 
 TYR   0.013   0.001   TYR A 360 
 PHE   0.012   0.001   PHE A 340 
 TRP   0.021   0.001   TRP B 297 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.01449 ( 6341)
  covalent geometry    : angle       0.95716 ( 8718)
  SS BOND              : bond        0.00235 (    1)
  SS BOND              : angle       0.69315 (    2)
  hydrogen bonds       : bond        0.15418 (  385)
  hydrogen bonds       : angle       5.75146 ( 1110)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.184 
Fit side-chains
REVERT: B  169 TRP cc_start: 0.8171 (m100) cc_final: 0.7909 (m100)
  outliers start: 6
  outliers final: 5
  residues processed: 72
  average time/residue: 0.0669
  time to fit residues: 6.7845
Evaluate side-chains
  66 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 271 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.110245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.095059 restraints weight = 13351.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.096983 restraints weight = 8046.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.098337 restraints weight = 5641.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.099410 restraints weight = 4325.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.100047 restraints weight = 3510.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.0761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6342  Z= 0.119
  Angle     :  0.449   5.399   8720  Z= 0.251
  Chirality :  0.039   0.164   1075
  Planarity :  0.003   0.028   1111
  Dihedral  :  4.487  38.063   1000
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 17.49 %
    Favored  : 79.67 %
  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 aren not related in a simple way.
  whole:  2.24 (0.29), residues: 913
  helix:  3.21 (0.25), residues: 413
  sheet:  0.65 (0.43), residues: 160
  loop : -0.32 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  49 
 TYR   0.011   0.001   TYR R 199 
 PHE   0.011   0.001   PHE B 235 
 TRP   0.009   0.001   TRP B 297 
 HIS   0.004   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 6341)
  covalent geometry    : angle       0.44923 ( 8718)
  SS BOND              : bond        0.00278 (    1)
  SS BOND              : angle       0.78642 (    2)
  hydrogen bonds       : bond        0.03919 (  385)
  hydrogen bonds       : angle       4.38732 ( 1110)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.184 
Fit side-chains
REVERT: R   82 MET cc_start: 0.7678 (ttm) cc_final: 0.7459 (ttp)
REVERT: R  296 HIS cc_start: 0.8411 (OUTLIER) cc_final: 0.8074 (p-80)
  outliers start: 12
  outliers final: 5
  residues processed: 77
  average time/residue: 0.0588
  time to fit residues: 6.5024
Evaluate side-chains
  64 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 22 optimal weight:    0.5980
   chunk 91 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 57 optimal weight:    8.9990
   chunk 25 optimal weight:    0.9980
   chunk 83 optimal weight:    0.9980
   chunk 60 optimal weight:    9.9990
   chunk 33 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0060
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.6596

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.110451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.095224 restraints weight = 13386.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.097171 restraints weight = 7995.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.098631 restraints weight = 5547.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.099473 restraints weight = 4220.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.100165 restraints weight = 3508.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.1053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6342  Z= 0.109
  Angle     :  0.431   5.389   8720  Z= 0.239
  Chirality :  0.039   0.152   1075
  Planarity :  0.003   0.028   1111
  Dihedral  :  4.268  38.616    995
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 18.68 %
    Favored  : 78.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.24 (0.29), residues: 913
  helix:  3.21 (0.25), residues: 420
  sheet:  0.71 (0.43), residues: 157
  loop : -0.42 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  49 
 TYR   0.011   0.001   TYR R 199 
 PHE   0.024   0.001   PHE A 340 
 TRP   0.016   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 6341)
  covalent geometry    : angle       0.43100 ( 8718)
  SS BOND              : bond        0.00251 (    1)
  SS BOND              : angle       0.71136 (    2)
  hydrogen bonds       : bond        0.03518 (  385)
  hydrogen bonds       : angle       3.99950 ( 1110)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.233 
Fit side-chains
REVERT: R  296 HIS cc_start: 0.8497 (OUTLIER) cc_final: 0.8259 (p-80)
  outliers start: 11
  outliers final: 7
  residues processed: 80
  average time/residue: 0.0580
  time to fit residues: 6.8071
Evaluate side-chains
  65 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  321 PHE
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 39 optimal weight:    4.9990
   chunk 87 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0570
   chunk 16 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 30 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9990
   chunk 89 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN
B 230 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.110542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.095271 restraints weight = 13423.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.097194 restraints weight = 8106.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.098653 restraints weight = 5691.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.099516 restraints weight = 4323.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.100263 restraints weight = 3581.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.1201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6342  Z= 0.105
  Angle     :  0.423   5.400   8720  Z= 0.233
  Chirality :  0.039   0.150   1075
  Planarity :  0.002   0.028   1111
  Dihedral  :  4.210  38.803    995
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 21.28 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.27 (0.29), residues: 913
  helix:  3.37 (0.25), residues: 414
  sheet:  0.62 (0.43), residues: 157
  loop : -0.49 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  49 
 TYR   0.017   0.001   TYR R 174 
 PHE   0.019   0.001   PHE A 340 
 TRP   0.018   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 6341)
  covalent geometry    : angle       0.42246 ( 8718)
  SS BOND              : bond        0.00234 (    1)
  SS BOND              : angle       0.64755 (    2)
  hydrogen bonds       : bond        0.03334 (  385)
  hydrogen bonds       : angle       3.86303 ( 1110)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.150 
Fit side-chains
REVERT: R  296 HIS cc_start: 0.8485 (OUTLIER) cc_final: 0.8276 (p-80)
  outliers start: 13
  outliers final: 9
  residues processed: 80
  average time/residue: 0.0600
  time to fit residues: 7.0372
Evaluate side-chains
  68 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  321 PHE
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 40 optimal weight:    0.0570
   chunk 13 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 5 optimal weight:   20.0000
   chunk 85 optimal weight:    0.0070
   chunk 11 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 83 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.9720

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.109219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.094037 restraints weight = 13731.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.095786 restraints weight = 8231.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.097370 restraints weight = 5791.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.098236 restraints weight = 4385.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.098499 restraints weight = 3634.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.1308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6342  Z= 0.135
  Angle     :  0.446   5.580   8720  Z= 0.247
  Chirality :  0.039   0.156   1075
  Planarity :  0.003   0.028   1111
  Dihedral  :  4.338  40.009    995
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 21.99 %
    Favored  : 74.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.25 (0.29), residues: 913
  helix:  3.41 (0.25), residues: 414
  sheet:  0.36 (0.42), residues: 161
  loop : -0.45 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  49 
 TYR   0.018   0.001   TYR R 174 
 PHE   0.014   0.001   PHE B 235 
 TRP   0.021   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 6341)
  covalent geometry    : angle       0.44564 ( 8718)
  SS BOND              : bond        0.00313 (    1)
  SS BOND              : angle       0.78413 (    2)
  hydrogen bonds       : bond        0.03438 (  385)
  hydrogen bonds       : angle       3.89019 ( 1110)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.171 
Fit side-chains
REVERT: R  275 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8678 (mm)
REVERT: R  296 HIS cc_start: 0.8498 (OUTLIER) cc_final: 0.8265 (p-80)
  outliers start: 15
  outliers final: 11
  residues processed: 75
  average time/residue: 0.0533
  time to fit residues: 5.8807
Evaluate side-chains
  71 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  321 PHE
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 87 optimal weight:    0.6980
   chunk 0 optimal weight:   20.0000
   chunk 11 optimal weight:    3.9990
   chunk 84 optimal weight:    0.5980
   chunk 20 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 14 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.109729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.094664 restraints weight = 13384.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.096550 restraints weight = 8052.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.097949 restraints weight = 5644.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.098821 restraints weight = 4312.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.099539 restraints weight = 3569.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.1400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6342  Z= 0.117
  Angle     :  0.429   5.485   8720  Z= 0.238
  Chirality :  0.039   0.164   1075
  Planarity :  0.003   0.028   1111
  Dihedral  :  4.282  39.659    995
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 22.70 %
    Favored  : 73.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.14 (0.29), residues: 913
  helix:  3.40 (0.25), residues: 414
  sheet: -0.07 (0.40), residues: 181
  loop : -0.39 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  49 
 TYR   0.020   0.001   TYR R 174 
 PHE   0.013   0.001   PHE B 235 
 TRP   0.021   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 6341)
  covalent geometry    : angle       0.42890 ( 8718)
  SS BOND              : bond        0.00258 (    1)
  SS BOND              : angle       0.69660 (    2)
  hydrogen bonds       : bond        0.03366 (  385)
  hydrogen bonds       : angle       3.83737 ( 1110)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.214 
Fit side-chains
REVERT: R  275 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8657 (mm)
REVERT: R  296 HIS cc_start: 0.8449 (OUTLIER) cc_final: 0.8231 (p-80)
  outliers start: 15
  outliers final: 11
  residues processed: 79
  average time/residue: 0.0623
  time to fit residues: 7.1209
Evaluate side-chains
  71 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  321 PHE
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 79 optimal weight:    0.8980
   chunk 89 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 57 optimal weight:    8.9990
   chunk 71 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 56 optimal weight:    0.3980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
B 230 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.109002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.093759 restraints weight = 13526.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.095696 restraints weight = 8115.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.097113 restraints weight = 5640.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.097956 restraints weight = 4305.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.098663 restraints weight = 3583.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.1454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6342  Z= 0.140
  Angle     :  0.449   6.279   8720  Z= 0.248
  Chirality :  0.039   0.170   1075
  Planarity :  0.003   0.028   1111
  Dihedral  :  4.391  40.418    995
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 22.93 %
    Favored  : 73.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.10 (0.29), residues: 913
  helix:  3.38 (0.25), residues: 414
  sheet: -0.12 (0.40), residues: 181
  loop : -0.42 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  49 
 TYR   0.022   0.001   TYR R 174 
 PHE   0.016   0.001   PHE B 235 
 TRP   0.022   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6341)
  covalent geometry    : angle       0.44907 ( 8718)
  SS BOND              : bond        0.00312 (    1)
  SS BOND              : angle       0.76599 (    2)
  hydrogen bonds       : bond        0.03448 (  385)
  hydrogen bonds       : angle       3.88425 ( 1110)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.151 
Fit side-chains
REVERT: R  275 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8693 (mm)
  outliers start: 14
  outliers final: 12
  residues processed: 74
  average time/residue: 0.0605
  time to fit residues: 6.3139
Evaluate side-chains
  73 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   99 TRP
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  321 PHE
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 6 optimal weight:    7.9990
   chunk 5 optimal weight:    8.9990
   chunk 16 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 2 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.108825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.093699 restraints weight = 13605.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.095668 restraints weight = 8188.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.096927 restraints weight = 5672.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.097948 restraints weight = 4391.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.098421 restraints weight = 3594.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.1531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6342  Z= 0.141
  Angle     :  0.451   5.579   8720  Z= 0.250
  Chirality :  0.039   0.177   1075
  Planarity :  0.003   0.036   1111
  Dihedral  :  4.426  40.511    995
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 22.93 %
    Favored  : 73.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.10 (0.29), residues: 913
  helix:  3.36 (0.25), residues: 414
  sheet: -0.11 (0.39), residues: 184
  loop : -0.38 (0.35), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 336 
 TYR   0.023   0.001   TYR R 174 
 PHE   0.016   0.001   PHE B 235 
 TRP   0.021   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 6341)
  covalent geometry    : angle       0.45074 ( 8718)
  SS BOND              : bond        0.00314 (    1)
  SS BOND              : angle       0.80366 (    2)
  hydrogen bonds       : bond        0.03501 (  385)
  hydrogen bonds       : angle       3.90303 ( 1110)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 0.210 
Fit side-chains
REVERT: R  275 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8711 (mm)
REVERT: R  296 HIS cc_start: 0.8408 (OUTLIER) cc_final: 0.7794 (p-80)
  outliers start: 15
  outliers final: 13
  residues processed: 75
  average time/residue: 0.0501
  time to fit residues: 5.6300
Evaluate side-chains
  73 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  321 PHE
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 52 optimal weight:    0.8980
   chunk 82 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.109072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.094002 restraints weight = 13600.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.095730 restraints weight = 8156.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.097237 restraints weight = 5739.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.098161 restraints weight = 4381.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.098715 restraints weight = 3613.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.1561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6342  Z= 0.126
  Angle     :  0.443   5.515   8720  Z= 0.243
  Chirality :  0.039   0.180   1075
  Planarity :  0.003   0.033   1111
  Dihedral  :  4.385  40.031    995
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 23.88 %
    Favored  : 72.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.16 (0.29), residues: 913
  helix:  3.43 (0.25), residues: 408
  sheet: -0.07 (0.39), residues: 184
  loop : -0.31 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  49 
 TYR   0.022   0.001   TYR R 174 
 PHE   0.015   0.001   PHE B 235 
 TRP   0.019   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6341)
  covalent geometry    : angle       0.44242 ( 8718)
  SS BOND              : bond        0.00272 (    1)
  SS BOND              : angle       0.73912 (    2)
  hydrogen bonds       : bond        0.03443 (  385)
  hydrogen bonds       : angle       3.86645 ( 1110)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.173 
Fit side-chains
REVERT: R  275 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8716 (mm)
REVERT: R  296 HIS cc_start: 0.8364 (OUTLIER) cc_final: 0.7605 (p-80)
  outliers start: 16
  outliers final: 12
  residues processed: 74
  average time/residue: 0.0484
  time to fit residues: 5.4018
Evaluate side-chains
  74 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   99 TRP
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 18 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 67 optimal weight:    0.6980
   chunk 61 optimal weight:    8.9990
   chunk 68 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 60 optimal weight:   10.0000
   chunk 42 optimal weight:    0.9990
   chunk 57 optimal weight:    5.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.108225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.093092 restraints weight = 13595.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.095021 restraints weight = 8252.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.096229 restraints weight = 5762.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.097194 restraints weight = 4484.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.097585 restraints weight = 3704.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.1627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6342  Z= 0.154
  Angle     :  0.468   7.069   8720  Z= 0.257
  Chirality :  0.039   0.155   1075
  Planarity :  0.003   0.034   1111
  Dihedral  :  4.505  40.917    995
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 24.59 %
    Favored  : 72.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.07 (0.29), residues: 913
  helix:  3.40 (0.25), residues: 413
  sheet: -0.12 (0.40), residues: 181
  loop : -0.48 (0.34), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 336 
 TYR   0.026   0.001   TYR R 174 
 PHE   0.017   0.001   PHE B 235 
 TRP   0.022   0.002   TRP B 169 
 HIS   0.006   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 6341)
  covalent geometry    : angle       0.46838 ( 8718)
  SS BOND              : bond        0.00343 (    1)
  SS BOND              : angle       0.83757 (    2)
  hydrogen bonds       : bond        0.03568 (  385)
  hydrogen bonds       : angle       3.94003 ( 1110)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.180 
Fit side-chains
REVERT: R   82 MET cc_start: 0.8432 (ttp) cc_final: 0.8020 (ttm)
REVERT: R  275 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8728 (mm)
REVERT: R  296 HIS cc_start: 0.8422 (OUTLIER) cc_final: 0.7703 (p-80)
  outliers start: 14
  outliers final: 12
  residues processed: 70
  average time/residue: 0.0585
  time to fit residues: 5.9489
Evaluate side-chains
  73 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   99 TRP
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 89 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 84 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.108172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.092978 restraints weight = 13586.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.094834 restraints weight = 8177.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.096204 restraints weight = 5766.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.096917 restraints weight = 4416.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.097560 restraints weight = 3731.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.1653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6342  Z= 0.151
  Angle     :  0.465   6.438   8720  Z= 0.256
  Chirality :  0.040   0.188   1075
  Planarity :  0.003   0.032   1111
  Dihedral  :  4.532  41.043    995
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 24.11 %
    Favored  : 72.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.02 (0.29), residues: 913
  helix:  3.36 (0.25), residues: 413
  sheet: -0.14 (0.40), residues: 181
  loop : -0.53 (0.34), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 336 
 TYR   0.026   0.001   TYR R 174 
 PHE   0.017   0.001   PHE B 235 
 TRP   0.020   0.002   TRP B 169 
 HIS   0.006   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 6341)
  covalent geometry    : angle       0.46491 ( 8718)
  SS BOND              : bond        0.00336 (    1)
  SS BOND              : angle       0.88444 (    2)
  hydrogen bonds       : bond        0.03552 (  385)
  hydrogen bonds       : angle       3.95079 ( 1110)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 898.47 seconds
wall clock time: 16 minutes 9.28 seconds (969.28 seconds total)