Starting phenix.real_space_refine
on Thu Jul  2 05:04:04 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7xbw_33107/07_2026/7xbw_33107.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xbw_33107/07_2026/7xbw_33107.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xbw_33107/07_2026/7xbw_33107.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xbw_33107/07_2026/7xbw_33107.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7xbw_33107/07_2026/7xbw_33107.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7xbw_33107/07_2026/7xbw_33107.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xbw_33107/07_2026/7xbw_33107.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xbw_33107/07_2026/7xbw_33107.map"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
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      42      5.16       5
     C    4316      2.51       5
     N    1087      2.21       5
     O    1218      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6663
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 1657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1657
          Classifications: {'peptide': 216}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 2, 'TRANS': 213}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 87
          Unresolved non-hydrogen angles: 99
          Unresolved non-hydrogen dihedrals: 77
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 5, 'HIS:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 41
    Chain: "D"
      Number of atoms: 2394
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2394
          Classifications: {'peptide': 329}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PTRANS': 5, 'TRANS': 323}
          Unresolved non-hydrogen bonds: 131
          Unresolved non-hydrogen angles: 153
          Unresolved non-hydrogen dihedrals: 109
          Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 3, 'ASN:plan1': 2, 'ARG:plan': 9, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 93
    Chain: "E"
      Number of atoms: 352
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 352
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 55
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 47
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 4}
          Unresolved non-hydrogen planarities: 34
    Chain: "R"
      Number of atoms: 2176
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2176
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PTRANS': 9, 'TRANS': 278}
          Unresolved non-hydrogen bonds: 163
          Unresolved non-hydrogen angles: 198
          Unresolved non-hydrogen dihedrals: 145
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 6, 'HIS:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 105
    Chain: "R"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 84
          Unusual residues: {'CLR': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.56, per 1000 atoms: 0.23
  Number of scatterers: 6663
  At special positions: 0
  Unit cell: (107.635, 111.815, 73.15, 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      42     16.00
     O    1218      8.00
     N    1087      7.00
     C    4316      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 102 " - pdb=" SG  CYS R 175 " 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: 0.48
  Conformation dependent library (CDL) restraints added in 288.4 milliseconds
  

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1676

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 8 sheets defined
      45.4% alpha, 17.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'C' and resid 6 through 32
    Processing helix  chain 'C' and resid 207 through 216
      removed outlier: 4.348A  pdb=" N   ILE C 212 " --> pdb=" O   LYS C 209 " (cutoff:3.500A)
      removed outlier: 5.593A  pdb=" N   HIS C 213 " --> pdb=" O   LYS C 210 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 228 through 230
      No H-bonds generated for 'chain 'C' and resid 228 through 230'
    Processing helix  chain 'C' and resid 242 through 255
    Processing helix  chain 'C' and resid 270 through 281
      removed outlier: 4.063A  pdb=" N   GLU C 276 " --> pdb=" O   ASP C 272 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   LYS C 279 " --> pdb=" O   GLU C 275 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 295 through 309
    Processing helix  chain 'C' and resid 327 through 349
      removed outlier: 4.333A  pdb=" N   ASN C 331 " --> pdb=" O   THR C 327 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 13 through 26
    Processing helix  chain 'D' and resid 29 through 34
    Processing helix  chain 'E' and resid 10 through 25
      removed outlier: 3.686A  pdb=" N   GLU E  17 " --> pdb=" O   ARG E  13 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 29 through 44
    Processing helix  chain 'E' and resid 45 through 48
    Processing helix  chain 'R' and resid 30 through 57
    Processing helix  chain 'R' and resid 64 through 92
      Proline residue:  R  85  - end of helix
    Processing helix  chain 'R' and resid 98 through 132
    Processing helix  chain 'R' and resid 133 through 140
    Processing helix  chain 'R' and resid 145 through 162
      removed outlier: 3.637A  pdb=" N   ILE R 149 " --> pdb=" O   HIS R 145 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 163 through 165
      No H-bonds generated for 'chain 'R' and resid 163 through 165'
    Processing helix  chain 'R' and resid 180 through 185
      removed outlier: 3.838A  pdb=" N   GLU R 185 " --> pdb=" O   GLU R 181 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 186 through 201
    Processing helix  chain 'R' and resid 201 through 221
      removed outlier: 3.503A  pdb=" N   LEU R 205 " --> pdb=" O   LEU R 201 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 227 through 259
      Proline residue:  R 246  - end of helix
    Processing helix  chain 'R' and resid 266 through 289
      removed outlier: 5.433A  pdb=" N   ARG R 272 " --> pdb=" O   ARG R 268 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   LEU R 273 " --> pdb=" O   LYS R 269 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 291 through 297
      removed outlier: 3.960A  pdb=" N   PHE R 295 " --> pdb=" O   LEU R 291 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 297 through 310
      removed outlier: 3.746A  pdb=" N   LYS R 310 " --> pdb=" O   HIS R 306 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 53 through 55
      removed outlier: 6.418A  pdb=" N   HIS C 188 " --> pdb=" O   LYS C  54 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL C 185 " --> pdb=" O   ASP C 200 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   LYS C  35 " --> pdb=" O   ALA C 220 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   ILE C 222 " --> pdb=" O   LYS C  35 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   LEU C  37 " --> pdb=" O   ILE C 222 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   CYS C 224 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   LEU C  39 " --> pdb=" O   CYS C 224 " (cutoff:3.500A)
      removed outlier: 8.682A  pdb=" N   ALA C 226 " --> pdb=" O   LEU C  39 " (cutoff:3.500A)
      removed outlier: 5.993A  pdb=" N   ILE C 221 " --> pdb=" O   ILE C 265 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   PHE C 267 " --> pdb=" O   ILE C 221 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   PHE C 223 " --> pdb=" O   PHE C 267 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   ASN C 269 " --> pdb=" O   PHE C 223 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   VAL C 225 " --> pdb=" O   ASN C 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 47 through 51
    Processing sheet with id=AA3, first strand: chain 'D' and resid 58 through 63
      removed outlier: 3.737A  pdb=" N   ALA D  60 " --> pdb=" O   ALA D  73 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ILE D  80 " --> pdb=" O   SER D  72 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   ILE D  81 " --> pdb=" O   VAL D  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 103 through 105
      removed outlier: 5.823A  pdb=" N   CYS D 121 " --> pdb=" O   GLU D 138 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   GLU D 138 " --> pdb=" O   CYS D 121 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ILE D 123 " --> pdb=" O   SER D 136 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ARG D 134 " --> pdb=" O   ASN D 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 146 through 151
      removed outlier: 3.678A  pdb=" N   THR D 178 " --> pdb=" O   LEU D 168 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   ASP D 170 " --> pdb=" O   GLN D 176 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   GLN D 176 " --> pdb=" O   ASP D 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 187 through 192
      removed outlier: 6.973A  pdb=" N   GLY D 202 " --> pdb=" O   MET D 188 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   LEU D 190 " --> pdb=" O   VAL D 200 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   VAL D 200 " --> pdb=" O   LEU D 190 " (cutoff:3.500A)
      removed outlier: 5.261A  pdb=" N   LEU D 192 " --> pdb=" O   LEU D 198 " (cutoff:3.500A)
      removed outlier: 7.472A  pdb=" N   LEU D 198 " --> pdb=" O   LEU D 192 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   SER D 201 " --> pdb=" O   LYS D 209 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LYS D 209 " --> pdb=" O   SER D 201 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   ALA D 203 " --> pdb=" O   SER D 207 " (cutoff:3.500A)
      removed outlier: 5.625A  pdb=" N   SER D 207 " --> pdb=" O   ALA D 203 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   GLN D 220 " --> pdb=" O   LEU D 210 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   ASP D 212 " --> pdb=" O   CYS D 218 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   CYS D 218 " --> pdb=" O   ASP D 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 229 through 234
      removed outlier: 3.776A  pdb=" N   MET D 262 " --> pdb=" O   LEU D 252 " (cutoff:3.500A)
      removed outlier: 7.409A  pdb=" N   ASP D 254 " --> pdb=" O   GLU D 260 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   GLU D 260 " --> pdb=" O   ASP D 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 273 through 278
      removed outlier: 6.943A  pdb=" N   VAL D 296 " --> pdb=" O   ALA D 305 " (cutoff:3.500A)

    368 hydrogen bonds defined for protein.
    1065 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.03

  Time building geometry restraints manager: 0.61 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2115
        1.34 -     1.46: 1643
        1.46 -     1.58: 2993
        1.58 -     1.70: 4
        1.70 -     1.81: 55
  Bond restraints: 6810
  Sorted by residual:
  bond pdb=" C5  CLR R 403 "
       pdb=" C6  CLR R 403 "
    ideal  model  delta    sigma   weight residual
    1.332  1.465 -0.133 2.00e-02 2.50e+03 4.40e+01
  bond pdb=" C5  CLR R 401 "
       pdb=" C6  CLR R 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.464 -0.132 2.00e-02 2.50e+03 4.36e+01
  bond pdb=" C5  CLR R 402 "
       pdb=" C6  CLR R 402 "
    ideal  model  delta    sigma   weight residual
    1.332  1.463 -0.131 2.00e-02 2.50e+03 4.31e+01
  bond pdb=" C3  CLR R 402 "
       pdb=" O1  CLR R 402 "
    ideal  model  delta    sigma   weight residual
    1.413  1.298  0.115 2.00e-02 2.50e+03 3.28e+01
  bond pdb=" C3  CLR R 401 "
       pdb=" O1  CLR R 401 "
    ideal  model  delta    sigma   weight residual
    1.413  1.299  0.114 2.00e-02 2.50e+03 3.23e+01
  ... (remaining 6805 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 9145
        1.73 -     3.45: 123
        3.45 -     5.18: 36
        5.18 -     6.90: 7
        6.90 -     8.63: 1
  Bond angle restraints: 9312
  Sorted by residual:
  angle pdb=" CA  PRO E  60 "
        pdb=" N   PRO E  60 "
        pdb=" CD  PRO E  60 "
      ideal   model   delta    sigma   weight residual
     112.00  106.71    5.29 1.40e+00 5.10e-01 1.43e+01
  angle pdb=" C   TYR R 259 "
        pdb=" N   ASP R 260 "
        pdb=" CA  ASP R 260 "
      ideal   model   delta    sigma   weight residual
     122.08  125.76   -3.68 1.47e+00 4.63e-01 6.27e+00
  angle pdb=" CA  LEU R  84 "
        pdb=" CB  LEU R  84 "
        pdb=" CG  LEU R  84 "
      ideal   model   delta    sigma   weight residual
     116.30  124.93   -8.63 3.50e+00 8.16e-02 6.08e+00
  angle pdb=" C   PRO E  60 "
        pdb=" CA  PRO E  60 "
        pdb=" CB  PRO E  60 "
      ideal   model   delta    sigma   weight residual
     110.00  112.72   -2.72 1.12e+00 7.97e-01 5.92e+00
  angle pdb=" C   PRO C 282 "
        pdb=" N   LEU C 283 "
        pdb=" CA  LEU C 283 "
      ideal   model   delta    sigma   weight residual
     121.54  126.14   -4.60 1.91e+00 2.74e-01 5.81e+00
  ... (remaining 9307 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.96: 3569
       14.96 -    29.91: 277
       29.91 -    44.87: 72
       44.87 -    59.82: 8
       59.82 -    74.78: 4
  Dihedral angle restraints: 3930
    sinusoidal: 1347
      harmonic: 2583
  Sorted by residual:
  dihedral pdb=" CA  ASP D 170 "
           pdb=" CB  ASP D 170 "
           pdb=" CG  ASP D 170 "
           pdb=" OD1 ASP D 170 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -81.40   51.40     1      2.00e+01 2.50e-03 9.03e+00
  dihedral pdb=" CA  CYS R 102 "
           pdb=" CB  CYS R 102 "
           pdb=" SG  CYS R 102 "
           pdb=" SG  CYS R 175 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00  129.88  -50.88     1      2.00e+01 2.50e-03 8.86e+00
  dihedral pdb=" CB  ARG D 150 "
           pdb=" CG  ARG D 150 "
           pdb=" CD  ARG D 150 "
           pdb=" NE  ARG D 150 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  106.56  -46.56     3      1.50e+01 4.44e-03 8.35e+00
  ... (remaining 3927 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 858
       0.043 -    0.087: 202
       0.087 -    0.130: 59
       0.130 -    0.173: 5
       0.173 -    0.217: 3
  Chirality restraints: 1127
  Sorted by residual:
  chirality pdb=" C14 CLR R 403 "
            pdb=" C13 CLR R 403 "
            pdb=" C15 CLR R 403 "
            pdb=" C8  CLR R 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.53    0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" C14 CLR R 401 "
            pdb=" C13 CLR R 401 "
            pdb=" C15 CLR R 401 "
            pdb=" C8  CLR R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.52    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" C14 CLR R 402 "
            pdb=" C13 CLR R 402 "
            pdb=" C15 CLR R 402 "
            pdb=" C8  CLR R 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.52    0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 1124 not shown)

  Planarity restraints: 1155
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D  38 "    0.053 5.00e-02 4.00e+02   8.07e-02 1.04e+01
        pdb=" N   PRO D  39 "   -0.140 5.00e-02 4.00e+02
        pdb=" CA  PRO D  39 "    0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO D  39 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN E  59 "    0.039 5.00e-02 4.00e+02   5.69e-02 5.18e+00
        pdb=" N   PRO E  60 "   -0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO E  60 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO E  60 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R  84 "    0.025 5.00e-02 4.00e+02   3.81e-02 2.33e+00
        pdb=" N   PRO R  85 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO R  85 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO R  85 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1152 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1388
        2.78 -     3.31: 6610
        3.31 -     3.84: 11485
        3.84 -     4.37: 13225
        4.37 -     4.90: 23050
  Nonbonded interactions: 55758
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D 274 "
            pdb=" O   VAL D 315 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OH  TYR R 179 "
            pdb=" NH1 ARG R 191 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" OG1 THR D  86 "
            pdb=" OD1 ASN D  88 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OD2 ASP C 200 "
            pdb=" OG1 THR C 202 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OH  TYR D 145 "
            pdb=" OD2 ASP D 186 "
     model   vdw
     2.288 3.040
  ... (remaining 55753 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.390
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7157
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      :  0.005   0.133   6811  Z= 0.245
  Angle     :  0.542   8.631   9314  Z= 0.271
  Chirality :  0.042   0.217   1127
  Planarity :  0.004   0.081   1155
  Dihedral  : 11.707  74.778   2251
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.47 (0.30), residues: 874
  helix:  2.46 (0.27), residues: 382
  sheet:  0.54 (0.41), residues: 178
  loop : -0.64 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  32 
 TYR   0.019   0.001   TYR R  90 
 PHE   0.020   0.001   PHE R 110 
 TRP   0.018   0.001   TRP D  82 
 HIS   0.004   0.001   HIS R 285 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00500 /  0.24 ( 6810)
  covalent geometry    : angle       0.54211 /  0.27 ( 9312)
  SS BOND              : bond        0.00231 /  0.12 (    1)
  SS BOND              : angle       1.07031 /  0.58 (    2)
  hydrogen bonds       : bond        0.16427 / 11.60 (  368)
  hydrogen bonds       : angle       5.97308 /  4.20 ( 1065)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.214 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.4193
  time to fit residues: 52.3642
Evaluate side-chains
  87 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    1.6386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  54 HIS
D  91 HIS
R 170 GLN
R 223 ASN
R 248 ASN
** R 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.179061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.133407 restraints weight = 6918.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 2.21
r_work: 0.3454 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.2964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061   6811  Z= 0.269
  Angle     :  0.664   9.373   9314  Z= 0.348
  Chirality :  0.045   0.162   1127
  Planarity :  0.004   0.063   1155
  Dihedral  :  5.049  58.706    957
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 13.62 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.28), residues: 874
  helix:  1.65 (0.26), residues: 392
  sheet:  0.02 (0.37), residues: 187
  loop : -0.55 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D  46 
 TYR   0.020   0.002   TYR D  59 
 PHE   0.029   0.003   PHE R 110 
 TRP   0.017   0.003   TRP C 258 
 HIS   0.008   0.002   HIS D 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00612 /  0.27 ( 6810)
  covalent geometry    : angle       0.66389 /  0.35 ( 9312)
  SS BOND              : bond        0.00326 /  0.17 (    1)
  SS BOND              : angle       2.04579 /  1.19 (    2)
  hydrogen bonds       : bond        0.04329 /  3.02 (  368)
  hydrogen bonds       : angle       5.07569 /  3.52 ( 1065)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.191 
Fit side-chains
REVERT: D   45 MET cc_start: 0.5937 (mmt) cc_final: 0.5382 (mmt)
REVERT: D  237 ASN cc_start: 0.7835 (t0) cc_final: 0.7620 (t0)
REVERT: R  288 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6447 (pt)
  outliers start: 19
  outliers final: 7
  residues processed: 128
  average time/residue: 0.3989
  time to fit residues: 54.3939
Evaluate side-chains
  108 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 GLU
Chi-restraints excluded: chain C residue  254 CYS
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain D residue   80 ILE
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  288 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 21 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9990
   chunk 46 optimal weight:    0.7980
   chunk 53 optimal weight:    8.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 188 HIS
D  54 HIS
** R  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 306 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.180860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.131475 restraints weight = 6769.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 2.18
r_work: 0.3467 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3312 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.3150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6811  Z= 0.164
  Angle     :  0.560  11.083   9314  Z= 0.289
  Chirality :  0.041   0.139   1127
  Planarity :  0.004   0.056   1155
  Dihedral  :  4.825  56.238    957
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 18.15 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.28), residues: 874
  helix:  1.76 (0.26), residues: 391
  sheet: -0.09 (0.39), residues: 175
  loop : -0.71 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  32 
 TYR   0.020   0.001   TYR R  90 
 PHE   0.024   0.002   PHE R 165 
 TRP   0.016   0.002   TRP D  82 
 HIS   0.009   0.001   HIS R 285 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00369 /  0.16 ( 6810)
  covalent geometry    : angle       0.55982 /  0.29 ( 9312)
  SS BOND              : bond        0.00134 /  0.07 (    1)
  SS BOND              : angle       1.80364 /  1.04 (    2)
  hydrogen bonds       : bond        0.03642 /  2.52 (  368)
  hydrogen bonds       : angle       4.72722 /  3.27 ( 1065)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.157 
Fit side-chains
REVERT: C  281 SER cc_start: 0.8132 (t) cc_final: 0.7899 (t)
REVERT: D  212 ASP cc_start: 0.8017 (t0) cc_final: 0.7795 (t0)
REVERT: D  263 THR cc_start: 0.8742 (OUTLIER) cc_final: 0.8445 (m)
REVERT: D  270 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7666 (pp)
REVERT: D  304 ARG cc_start: 0.8071 (mtt90) cc_final: 0.7809 (ttm170)
REVERT: R   49 ASN cc_start: 0.5848 (m-40) cc_final: 0.5582 (m110)
REVERT: R  288 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6349 (pt)
  outliers start: 20
  outliers final: 6
  residues processed: 120
  average time/residue: 0.4499
  time to fit residues: 57.2426
Evaluate side-chains
  104 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  254 CYS
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain R residue   88 THR
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  198 LEU
Chi-restraints excluded: chain R residue  238 ILE
Chi-restraints excluded: chain R residue  288 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0770
   chunk 78 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 8 optimal weight:    0.7980
   chunk 75 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 60 optimal weight:    2.9990
   overall best weight:    0.6740

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 340 ASN
** R  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.179727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.136079 restraints weight = 6999.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 2.11
r_work: 0.3408 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3261 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.3252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6811  Z= 0.144
  Angle     :  0.545   9.818   9314  Z= 0.283
  Chirality :  0.040   0.137   1127
  Planarity :  0.003   0.050   1155
  Dihedral  :  4.646  54.688    957
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 18.61 %
    Favored  : 77.76 %
  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 are not related in a simple way.
  whole:  0.76 (0.28), residues: 874
  helix:  1.89 (0.26), residues: 390
  sheet: -0.25 (0.38), residues: 175
  loop : -0.79 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  32 
 TYR   0.020   0.001   TYR R  90 
 PHE   0.018   0.001   PHE R 165 
 TRP   0.016   0.001   TRP D  82 
 HIS   0.009   0.001   HIS R 285 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.14 ( 6810)
  covalent geometry    : angle       0.54461 /  0.28 ( 9312)
  SS BOND              : bond        0.00083 /  0.04 (    1)
  SS BOND              : angle       1.75611 /  1.01 (    2)
  hydrogen bonds       : bond        0.03383 /  2.33 (  368)
  hydrogen bonds       : angle       4.57016 /  3.15 ( 1065)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 106
  time to evaluate  : 0.246 
Fit side-chains
REVERT: C  281 SER cc_start: 0.8234 (t) cc_final: 0.8029 (t)
REVERT: D  263 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8413 (m)
REVERT: D  270 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7719 (pp)
REVERT: R   49 ASN cc_start: 0.5892 (m-40) cc_final: 0.5620 (m110)
REVERT: R  288 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6353 (pt)
  outliers start: 24
  outliers final: 11
  residues processed: 118
  average time/residue: 0.4627
  time to fit residues: 57.9452
Evaluate side-chains
  108 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 GLU
Chi-restraints excluded: chain C residue  254 CYS
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain D residue   80 ILE
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain R residue   88 THR
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  238 ILE
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain R residue  288 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 35 optimal weight:    0.0470
   chunk 42 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 75 optimal weight:    0.8980
   chunk 64 optimal weight:    6.9990
   chunk 41 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.6078

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.180177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.136675 restraints weight = 7038.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 2.14
r_work: 0.3415 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3266 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.3353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6811  Z= 0.137
  Angle     :  0.546  11.795   9314  Z= 0.282
  Chirality :  0.040   0.135   1127
  Planarity :  0.003   0.047   1155
  Dihedral  :  4.635  54.464    957
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 20.57 %
    Favored  : 76.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.28), residues: 874
  helix:  1.92 (0.26), residues: 391
  sheet: -0.20 (0.38), residues: 177
  loop : -0.75 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  32 
 TYR   0.021   0.001   TYR R  90 
 PHE   0.026   0.001   PHE R 165 
 TRP   0.014   0.001   TRP D  82 
 HIS   0.008   0.001   HIS R 285 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.14 ( 6810)
  covalent geometry    : angle       0.54591 /  0.28 ( 9312)
  SS BOND              : bond        0.00083 /  0.04 (    1)
  SS BOND              : angle       1.75416 /  1.01 (    2)
  hydrogen bonds       : bond        0.03281 /  2.26 (  368)
  hydrogen bonds       : angle       4.47777 /  3.09 ( 1065)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.309 
Fit side-chains
REVERT: D   46 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7281 (mmm160)
REVERT: D  263 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8419 (m)
REVERT: R   49 ASN cc_start: 0.5889 (m-40) cc_final: 0.5612 (m110)
REVERT: R  288 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6310 (pt)
  outliers start: 21
  outliers final: 14
  residues processed: 113
  average time/residue: 0.4869
  time to fit residues: 58.4432
Evaluate side-chains
  110 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 GLU
Chi-restraints excluded: chain C residue  254 CYS
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain D residue   46 ARG
Chi-restraints excluded: chain D residue   80 ILE
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain R residue   88 THR
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  238 ILE
Chi-restraints excluded: chain R residue  242 LEU
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain R residue  288 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 79 optimal weight:    0.6980
   chunk 81 optimal weight:    0.6980
   chunk 63 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0970
   chunk 66 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 21 optimal weight:    7.9990
   overall best weight:    0.6578

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.178970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.134899 restraints weight = 7015.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 2.16
r_work: 0.3423 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3273 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.3495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6811  Z= 0.140
  Angle     :  0.545  10.904   9314  Z= 0.282
  Chirality :  0.040   0.133   1127
  Planarity :  0.003   0.045   1155
  Dihedral  :  4.678  54.011    957
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 20.57 %
    Favored  : 75.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.28), residues: 874
  helix:  1.92 (0.26), residues: 392
  sheet: -0.23 (0.38), residues: 175
  loop : -0.80 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  32 
 TYR   0.021   0.001   TYR R  90 
 PHE   0.016   0.001   PHE R 165 
 TRP   0.015   0.001   TRP D  82 
 HIS   0.008   0.001   HIS R 285 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00310 /  0.14 ( 6810)
  covalent geometry    : angle       0.54446 /  0.28 ( 9312)
  SS BOND              : bond        0.00015 /  0.01 (    1)
  SS BOND              : angle       1.82338 /  1.05 (    2)
  hydrogen bonds       : bond        0.03251 /  2.24 (  368)
  hydrogen bonds       : angle       4.45297 /  3.07 ( 1065)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 105
  time to evaluate  : 0.247 
Fit side-chains
REVERT: C  276 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7202 (pm20)
REVERT: D   46 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7301 (mmm160)
REVERT: D  270 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7727 (pp)
REVERT: R   49 ASN cc_start: 0.5867 (m-40) cc_final: 0.5594 (m110)
REVERT: R  288 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6494 (pt)
  outliers start: 27
  outliers final: 16
  residues processed: 123
  average time/residue: 0.4335
  time to fit residues: 56.8266
Evaluate side-chains
  113 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 GLU
Chi-restraints excluded: chain C residue  254 CYS
Chi-restraints excluded: chain C residue  276 GLU
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain D residue   46 ARG
Chi-restraints excluded: chain D residue   80 ILE
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain R residue   32 VAL
Chi-restraints excluded: chain R residue   88 THR
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  238 ILE
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain R residue  288 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 40 optimal weight:    0.4980
   chunk 82 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 69 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 59 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 269 ASN
** D  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.177712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.134887 restraints weight = 6939.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 2.05
r_work: 0.3457 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3308 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.3628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6811  Z= 0.153
  Angle     :  0.564  10.208   9314  Z= 0.294
  Chirality :  0.040   0.133   1127
  Planarity :  0.003   0.043   1155
  Dihedral  :  4.785  54.523    957
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 21.79 %
    Favored  : 74.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.28), residues: 874
  helix:  1.91 (0.26), residues: 391
  sheet: -0.15 (0.38), residues: 169
  loop : -0.90 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  32 
 TYR   0.022   0.001   TYR R  90 
 PHE   0.025   0.002   PHE R 165 
 TRP   0.014   0.001   TRP D  82 
 HIS   0.008   0.001   HIS R 285 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00341 /  0.15 ( 6810)
  covalent geometry    : angle       0.56300 /  0.29 ( 9312)
  SS BOND              : bond        0.00048 /  0.03 (    1)
  SS BOND              : angle       1.96250 /  1.13 (    2)
  hydrogen bonds       : bond        0.03342 /  2.31 (  368)
  hydrogen bonds       : angle       4.47003 /  3.08 ( 1065)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.250 
Fit side-chains
REVERT: C  276 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6671 (pm20)
REVERT: D   46 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7339 (mmm160)
REVERT: D  270 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7871 (pp)
REVERT: R   49 ASN cc_start: 0.5973 (m-40) cc_final: 0.5679 (m110)
REVERT: R  103 LYS cc_start: 0.6843 (ttmm) cc_final: 0.6498 (mmtm)
REVERT: R  192 ASN cc_start: 0.7122 (m-40) cc_final: 0.6915 (m-40)
REVERT: R  288 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6530 (pt)
  outliers start: 27
  outliers final: 19
  residues processed: 124
  average time/residue: 0.4246
  time to fit residues: 56.1752
Evaluate side-chains
  119 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 GLU
Chi-restraints excluded: chain C residue  254 CYS
Chi-restraints excluded: chain C residue  276 GLU
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain D residue   46 ARG
Chi-restraints excluded: chain D residue   80 ILE
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain R residue   32 VAL
Chi-restraints excluded: chain R residue   88 THR
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  238 ILE
Chi-restraints excluded: chain R residue  242 LEU
Chi-restraints excluded: chain R residue  286 CYS
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain R residue  288 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 12 optimal weight:    0.2980
   chunk 71 optimal weight:    0.9990
   chunk 68 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 59 optimal weight:    4.9990
   chunk 11 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 58 optimal weight:   10.0000
   chunk 38 optimal weight:    2.9990
   chunk 72 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 269 ASN
D  54 HIS
** R  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 139 ASN
** R 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.178665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.134287 restraints weight = 6987.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3575 rms_B_bonded: 2.06
r_work: 0.3432 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3286 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.3663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6811  Z= 0.136
  Angle     :  0.559  12.482   9314  Z= 0.289
  Chirality :  0.040   0.136   1127
  Planarity :  0.003   0.042   1155
  Dihedral  :  4.737  55.002    957
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 21.48 %
    Favored  : 74.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.29), residues: 874
  helix:  1.94 (0.26), residues: 392
  sheet:  0.00 (0.38), residues: 176
  loop : -0.89 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C  32 
 TYR   0.024   0.001   TYR R  90 
 PHE   0.017   0.001   PHE R 165 
 TRP   0.015   0.001   TRP D  82 
 HIS   0.008   0.001   HIS R 285 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.14 ( 6810)
  covalent geometry    : angle       0.55880 /  0.29 ( 9312)
  SS BOND              : bond        0.00008 /  0.00 (    1)
  SS BOND              : angle       1.87181 /  1.07 (    2)
  hydrogen bonds       : bond        0.03238 /  2.23 (  368)
  hydrogen bonds       : angle       4.40461 /  3.03 ( 1065)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 101
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: C  276 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6548 (pm20)
REVERT: D  269 ILE cc_start: 0.6422 (OUTLIER) cc_final: 0.6141 (pp)
REVERT: R   49 ASN cc_start: 0.5998 (m-40) cc_final: 0.5717 (m110)
REVERT: R  288 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6650 (pt)
  outliers start: 29
  outliers final: 16
  residues processed: 121
  average time/residue: 0.4142
  time to fit residues: 53.5402
Evaluate side-chains
  110 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 GLU
Chi-restraints excluded: chain C residue  254 CYS
Chi-restraints excluded: chain C residue  276 GLU
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain D residue   80 ILE
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  269 ILE
Chi-restraints excluded: chain R residue   32 VAL
Chi-restraints excluded: chain R residue   88 THR
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  238 ILE
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain R residue  288 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 46 optimal weight:    0.0870
   chunk 30 optimal weight:    0.6980
   chunk 79 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 73 optimal weight:    8.9990
   chunk 58 optimal weight:    9.9990
   chunk 5 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0670
   overall best weight:    0.6898

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 237 ASN
** R  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  72 ASN
** R 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.177915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.136127 restraints weight = 6991.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3671 rms_B_bonded: 1.98
r_work: 0.3473 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3325 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.3750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6811  Z= 0.147
  Angle     :  0.581  12.391   9314  Z= 0.298
  Chirality :  0.041   0.133   1127
  Planarity :  0.003   0.044   1155
  Dihedral  :  4.836  55.993    957
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 22.39 %
    Favored  : 73.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.29), residues: 874
  helix:  1.95 (0.27), residues: 385
  sheet: -0.05 (0.38), residues: 176
  loop : -0.90 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG C  32 
 TYR   0.012   0.001   TYR R  90 
 PHE   0.023   0.002   PHE R 165 
 TRP   0.015   0.001   TRP D  82 
 HIS   0.008   0.001   HIS R 285 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.15 ( 6810)
  covalent geometry    : angle       0.57999 /  0.30 ( 9312)
  SS BOND              : bond        0.00053 /  0.03 (    1)
  SS BOND              : angle       2.04438 /  1.17 (    2)
  hydrogen bonds       : bond        0.03279 /  2.27 (  368)
  hydrogen bonds       : angle       4.43005 /  3.05 ( 1065)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 95
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
REVERT: C  251 ASP cc_start: 0.8242 (t0) cc_final: 0.8038 (t0)
REVERT: C  276 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6521 (pm20)
REVERT: D  269 ILE cc_start: 0.6370 (OUTLIER) cc_final: 0.6137 (pp)
REVERT: R   49 ASN cc_start: 0.5997 (m-40) cc_final: 0.5695 (m110)
REVERT: R  103 LYS cc_start: 0.6907 (ttmm) cc_final: 0.6581 (mmtm)
REVERT: R  165 PHE cc_start: 0.7606 (p90) cc_final: 0.7379 (p90)
REVERT: R  288 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6619 (pt)
  outliers start: 26
  outliers final: 18
  residues processed: 111
  average time/residue: 0.3720
  time to fit residues: 44.3345
Evaluate side-chains
  112 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 GLU
Chi-restraints excluded: chain C residue  254 CYS
Chi-restraints excluded: chain C residue  276 GLU
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain D residue   80 ILE
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  269 ILE
Chi-restraints excluded: chain R residue   32 VAL
Chi-restraints excluded: chain R residue   88 THR
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  238 ILE
Chi-restraints excluded: chain R residue  286 CYS
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain R residue  288 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 58 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 79 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 237 ASN
D 340 ASN
** R  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.177033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.133942 restraints weight = 6995.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 2.14
r_work: 0.3471 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3321 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.3862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6811  Z= 0.156
  Angle     :  0.591  12.066   9314  Z= 0.305
  Chirality :  0.041   0.134   1127
  Planarity :  0.004   0.045   1155
  Dihedral  :  4.959  58.147    957
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 23.15 %
    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 are not related in a simple way.
  whole:  0.79 (0.29), residues: 874
  helix:  1.94 (0.27), residues: 385
  sheet: -0.08 (0.38), residues: 176
  loop : -0.88 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C  32 
 TYR   0.025   0.001   TYR R  90 
 PHE   0.026   0.002   PHE R 165 
 TRP   0.014   0.001   TRP D  82 
 HIS   0.007   0.001   HIS R 285 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.16 ( 6810)
  covalent geometry    : angle       0.59064 /  0.30 ( 9312)
  SS BOND              : bond        0.00010 /  0.01 (    1)
  SS BOND              : angle       2.09910 /  1.20 (    2)
  hydrogen bonds       : bond        0.03361 /  2.32 (  368)
  hydrogen bonds       : angle       4.47431 /  3.08 ( 1065)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.263 
Fit side-chains
REVERT: C  186 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7821 (tm-30)
REVERT: C  197 LYS cc_start: 0.8736 (mtpt) cc_final: 0.8350 (mtpp)
REVERT: C  251 ASP cc_start: 0.8205 (t0) cc_final: 0.8000 (t0)
REVERT: C  276 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6514 (pm20)
REVERT: D  269 ILE cc_start: 0.6264 (OUTLIER) cc_final: 0.6061 (pp)
REVERT: R   49 ASN cc_start: 0.5981 (m-40) cc_final: 0.5686 (m110)
REVERT: R  166 MET cc_start: 0.7645 (ptt) cc_final: 0.7298 (ptp)
REVERT: R  288 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6648 (pt)
  outliers start: 22
  outliers final: 17
  residues processed: 112
  average time/residue: 0.3911
  time to fit residues: 47.0076
Evaluate side-chains
  116 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 GLU
Chi-restraints excluded: chain C residue  254 CYS
Chi-restraints excluded: chain C residue  276 GLU
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain D residue   80 ILE
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  269 ILE
Chi-restraints excluded: chain R residue   32 VAL
Chi-restraints excluded: chain R residue   88 THR
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  286 CYS
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain R residue  288 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 76 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 80 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 72 optimal weight:    0.1980
   chunk 51 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 306 GLN
** D  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 237 ASN
** R  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 139 ASN
** R 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.172750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.124097 restraints weight = 7009.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 2.18
r_work: 0.3407 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3255 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.3890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6811  Z= 0.149
  Angle     :  0.584  12.071   9314  Z= 0.301
  Chirality :  0.040   0.135   1127
  Planarity :  0.003   0.045   1155
  Dihedral  :  5.000  59.423    957
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 23.45 %
    Favored  : 73.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.29), residues: 874
  helix:  1.89 (0.26), residues: 391
  sheet: -0.11 (0.38), residues: 177
  loop : -0.88 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG C  32 
 TYR   0.013   0.001   TYR R  90 
 PHE   0.031   0.002   PHE R 295 
 TRP   0.013   0.001   TRP D  82 
 HIS   0.007   0.001   HIS R 285 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00335 /  0.15 ( 6810)
  covalent geometry    : angle       0.58363 /  0.30 ( 9312)
  SS BOND              : bond        0.00010 /  0.01 (    1)
  SS BOND              : angle       2.06060 /  1.18 (    2)
  hydrogen bonds       : bond        0.03344 /  2.31 (  368)
  hydrogen bonds       : angle       4.48288 /  3.08 ( 1065)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3282.60 seconds
wall clock time: 56 minutes 37.82 seconds (3397.82 seconds total)