Starting phenix.real_space_refine
on Sun Apr  5 04:33:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9x22_66470/04_2026/9x22_66470_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9x22_66470/04_2026/9x22_66470.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9x22_66470/04_2026/9x22_66470.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9x22_66470/04_2026/9x22_66470.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9x22_66470/04_2026/9x22_66470_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9x22_66470/04_2026/9x22_66470_neut.cif"
  }
  resolution = 2.92
  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=   0.063
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      49      5.16       5
     C    5144      2.51       5
     N    1385      2.21       5
     O    1465      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8043
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "P"
      Number of atoms: 233
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 233
          Classifications: {'peptide': 30}
          Link IDs: {'TRANS': 29}
    Chain: "R"
      Number of atoms: 3131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 3131
          Classifications: {'peptide': 384}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 14, 'TRANS': 369}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 29
    Chain: "A"
      Number of atoms: 1650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1650
          Classifications: {'peptide': 211}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 4, 'TRANS': 206}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 85
          Unresolved non-hydrogen angles: 100
          Unresolved non-hydrogen dihedrals: 72
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4, 'PHE:plan': 1, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 54
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 429
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
  Time building chain proxies: 1.40, per 1000 atoms: 0.17
  Number of scatterers: 8043
  At special positions: 0
  Unit cell: (78.183, 101.745, 175.644, 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      49     16.00
     O    1465      8.00
     N    1385      7.00
     C    5144      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  46 " - pdb=" SG  CYS R  71 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  85 " - pdb=" SG  CYS R 126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 226 " - pdb=" SG  CYS R 296 " distance=2.03

  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: 0.68
  Conformation dependent library (CDL) restraints added in 298.8 milliseconds
  

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1930

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 10 sheets defined
      46.1% alpha, 15.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'P' and resid 7 through 35
    Processing helix  chain 'R' and resid 31 through 53
    Processing helix  chain 'R' and resid 112 through 116
    Processing helix  chain 'R' and resid 137 through 169
    Processing helix  chain 'R' and resid 174 through 205
    Processing helix  chain 'R' and resid 206 through 216
    Processing helix  chain 'R' and resid 219 through 223
    Processing helix  chain 'R' and resid 224 through 257
      removed outlier: 3.726A  pdb=" N   GLN R 234 " --> pdb=" O   PHE R 230 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 261 through 275
    Processing helix  chain 'R' and resid 275 through 291
      removed outlier: 3.652A  pdb=" N   LEU R 279 " --> pdb=" O   GLY R 275 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   PHE R 280 " --> pdb=" O   VAL R 276 " (cutoff:3.500A)
      Proline residue:  R 283  - end of helix
    Processing helix  chain 'R' and resid 306 through 337
      Proline residue:  R 312  - end of helix
    Processing helix  chain 'R' and resid 345 through 357
    Processing helix  chain 'R' and resid 361 through 363
      No H-bonds generated for 'chain 'R' and resid 361 through 363'
    Processing helix  chain 'R' and resid 364 through 369
      removed outlier: 4.695A  pdb=" N   PHE R 369 " --> pdb=" O   VAL R 365 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 377 through 404
      removed outlier: 4.194A  pdb=" N   GLY R 395 " --> pdb=" O   THR R 391 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   LEU R 396 " --> pdb=" O   SER R 392 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 406 through 423
    Processing helix  chain 'A' and resid 6 through 28
    Processing helix  chain 'A' and resid 230 through 243
    Processing helix  chain 'A' and resid 258 through 269
    Processing helix  chain 'A' and resid 272 through 277
      removed outlier: 4.035A  pdb=" N   TYR A 276 " --> pdb=" O   LYS A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 281
    Processing helix  chain 'A' and resid 297 through 316
    Processing helix  chain 'A' and resid 335 through 356
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 8 through 24
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.567A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   HIS G  44 " --> pdb=" O   TYR G  40 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.681A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing sheet with id=AA1, first strand: chain 'R' and resid 65 through 66
    Processing sheet with id=AA2, first strand: chain 'R' and resid 81 through 84
      removed outlier: 3.661A  pdb=" N   VAL R  81 " --> pdb=" O   ARG R 102 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 189
      removed outlier: 6.582A  pdb=" N   LEU A  34 " --> pdb=" O   HIS A 195 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   PHE A 197 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 197 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 218 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   ILE A 220 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 220 " (cutoff:3.500A)
      removed outlier: 7.755A  pdb=" N   VAL A 222 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   ILE A 219 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   PHE A 255 " --> pdb=" O   ILE A 219 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   PHE A 221 " --> pdb=" O   PHE A 255 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   ASN A 257 " --> pdb=" O   PHE A 221 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   VAL A 223 " --> pdb=" O   ASN A 257 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 52
      removed outlier: 6.527A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.101A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.877A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.846A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.878A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.024A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.684A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.943A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.265A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.894A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.750A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.536A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    426 hydrogen bonds defined for protein.
    1248 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: 1.13

  Time building geometry restraints manager: 0.92 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2609
        1.34 -     1.46: 1882
        1.46 -     1.58: 3667
        1.58 -     1.69: 0
        1.69 -     1.81: 66
  Bond restraints: 8224
  Sorted by residual:
  bond pdb=" C   SER B  67 "
       pdb=" N   ARG B  68 "
    ideal  model  delta    sigma   weight residual
    1.332  1.316  0.017 1.40e-02 5.10e+03 1.45e+00
  bond pdb=" CB  ASP A 227 "
       pdb=" CG  ASP A 227 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 2.50e-02 1.60e+03 1.21e+00
  bond pdb=" CA  TYR R  88 "
       pdb=" CB  TYR R  88 "
    ideal  model  delta    sigma   weight residual
    1.535  1.550 -0.015 1.37e-02 5.33e+03 1.15e+00
  bond pdb=" CB  MET R 204 "
       pdb=" CG  MET R 204 "
    ideal  model  delta    sigma   weight residual
    1.520  1.490  0.030 3.00e-02 1.11e+03 1.02e+00
  bond pdb=" SD  MET R 204 "
       pdb=" CE  MET R 204 "
    ideal  model  delta    sigma   weight residual
    1.791  1.766  0.025 2.50e-02 1.60e+03 9.65e-01
  ... (remaining 8219 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 10966
        1.76 -     3.52: 174
        3.52 -     5.28: 18
        5.28 -     7.04: 5
        7.04 -     8.79: 2
  Bond angle restraints: 11165
  Sorted by residual:
  angle pdb=" C   MET R 204 "
        pdb=" CA  MET R 204 "
        pdb=" CB  MET R 204 "
      ideal   model   delta    sigma   weight residual
     110.88  105.60    5.28 1.57e+00 4.06e-01 1.13e+01
  angle pdb=" N   LEU R 224 "
        pdb=" CA  LEU R 224 "
        pdb=" C   LEU R 224 "
      ideal   model   delta    sigma   weight residual
     114.31  110.16    4.15 1.29e+00 6.01e-01 1.04e+01
  angle pdb=" N   ALA A  30 "
        pdb=" CA  ALA A  30 "
        pdb=" C   ALA A  30 "
      ideal   model   delta    sigma   weight residual
     113.88  110.14    3.74 1.23e+00 6.61e-01 9.23e+00
  angle pdb=" CA  TYR R  88 "
        pdb=" CB  TYR R  88 "
        pdb=" CG  TYR R  88 "
      ideal   model   delta    sigma   weight residual
     113.90  119.28   -5.38 1.80e+00 3.09e-01 8.93e+00
  angle pdb=" CB  MET R 204 "
        pdb=" CG  MET R 204 "
        pdb=" SD  MET R 204 "
      ideal   model   delta    sigma   weight residual
     112.70  103.91    8.79 3.00e+00 1.11e-01 8.59e+00
  ... (remaining 11160 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.99: 4163
       16.99 -    33.99: 525
       33.99 -    50.98: 119
       50.98 -    67.97: 23
       67.97 -    84.97: 6
  Dihedral angle restraints: 4836
    sinusoidal: 1862
      harmonic: 2974
  Sorted by residual:
  dihedral pdb=" CB  CYS R 226 "
           pdb=" SG  CYS R 226 "
           pdb=" SG  CYS R 296 "
           pdb=" CB  CYS R 296 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  123.59  -30.59     1      1.00e+01 1.00e-02 1.34e+01
  dihedral pdb=" CG  ARG R 326 "
           pdb=" CD  ARG R 326 "
           pdb=" NE  ARG R 326 "
           pdb=" CZ  ARG R 326 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.80   44.20     2      1.50e+01 4.44e-03 1.04e+01
  dihedral pdb=" CB  GLU R  41 "
           pdb=" CG  GLU R  41 "
           pdb=" CD  GLU R  41 "
           pdb=" OE1 GLU R  41 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   84.97  -84.97     1      3.00e+01 1.11e-03 9.73e+00
  ... (remaining 4833 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 726
       0.027 -    0.054: 324
       0.054 -    0.081: 120
       0.081 -    0.109: 61
       0.109 -    0.136: 23
  Chirality restraints: 1254
  Sorted by residual:
  chirality pdb=" CA  TYR R 148 "
            pdb=" N   TYR R 148 "
            pdb=" C   TYR R 148 "
            pdb=" CB  TYR R 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.60e-01
  chirality pdb=" CA  ILE A 253 "
            pdb=" N   ILE A 253 "
            pdb=" C   ILE A 253 "
            pdb=" CB  ILE A 253 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.98e-01
  chirality pdb=" CA  VAL R 370 "
            pdb=" N   VAL R 370 "
            pdb=" C   VAL R 370 "
            pdb=" CB  VAL R 370 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.81e-01
  ... (remaining 1251 not shown)

  Planarity restraints: 1412
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R  33 "   -0.014 2.00e-02 2.50e+03   1.47e-02 5.37e+00
        pdb=" CG  TRP R  33 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 TRP R  33 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD2 TRP R  33 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP R  33 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP R  33 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP R  33 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R  33 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R  33 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP R  33 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R 357 "    0.037 5.00e-02 4.00e+02   5.69e-02 5.18e+00
        pdb=" N   PRO R 358 "   -0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO R 358 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO R 358 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 276 "   -0.029 5.00e-02 4.00e+02   4.36e-02 3.04e+00
        pdb=" N   PRO R 277 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO R 277 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO R 277 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1409 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 223
        2.70 -     3.25: 7847
        3.25 -     3.80: 13177
        3.80 -     4.35: 16735
        4.35 -     4.90: 28278
  Nonbonded interactions: 66260
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" OE2 GLU R 292 "
            pdb=" OG  SER R 301 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" OG  SER R 155 "
            pdb=" O   SER R 392 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OE1 GLN B 176 "
            pdb=" OG1 THR B 179 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   VAL A 311 "
            pdb=" OG  SER A 314 "
     model   vdw
     2.288 3.040
  ... (remaining 66255 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=0.00 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:             1.190
  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:          0.130
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  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:6.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
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      :  0.003   0.032   8227  Z= 0.136
  Angle     :  0.554   8.794  11171  Z= 0.332
  Chirality :  0.040   0.136   1254
  Planarity :  0.004   0.057   1412
  Dihedral  : 15.696  84.968   2897
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.11 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 18.63 %
    Favored  : 79.48 %
  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:  1.01 (0.27), residues: 997
  helix:  2.30 (0.25), residues: 435
  sheet: -0.32 (0.38), residues: 189
  loop : -0.73 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  31 
 TYR   0.021   0.002   TYR R 148 
 PHE   0.021   0.001   PHE R 230 
 TRP   0.040   0.002   TRP R  33 
 HIS   0.010   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 8224)
  covalent geometry    : angle       0.55329 (11165)
  SS BOND              : bond        0.00256 (    3)
  SS BOND              : angle       0.90959 (    6)
  hydrogen bonds       : bond        0.16535 (  426)
  hydrogen bonds       : angle       5.69576 ( 1248)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
REVERT: A  196 MET cc_start: 0.7607 (ttp) cc_final: 0.7354 (ttp)
  outliers start: 16
  outliers final: 13
  residues processed: 87
  average time/residue: 0.4374
  time to fit residues: 41.0800
Evaluate side-chains
  88 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  174 CYS
Chi-restraints excluded: chain R residue  211 GLN
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.2980
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:   30.0000
   chunk 33 optimal weight:    0.0070
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.0570
   overall best weight:    0.3716

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

Flipped N/Q/H residues before XYZ refinement:
P   7 HIS
A 214 ASN
B  88 ASN
B 155 ASN
B 266 HIS
G  44 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.221453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.156169 restraints weight = 8584.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 2.15
r_work: 0.3347 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.0800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8227  Z= 0.109
  Angle     :  0.478   8.213  11171  Z= 0.258
  Chirality :  0.040   0.141   1254
  Planarity :  0.004   0.051   1412
  Dihedral  :  5.224  58.089   1129
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.31 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.81 %
    Favored  : 79.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.27), residues: 997
  helix:  2.50 (0.24), residues: 432
  sheet: -0.13 (0.39), residues: 181
  loop : -0.73 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  31 
 TYR   0.020   0.001   TYR R 148 
 PHE   0.019   0.001   PHE R 230 
 TRP   0.015   0.001   TRP R  33 
 HIS   0.008   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 8224)
  covalent geometry    : angle       0.47749 (11165)
  SS BOND              : bond        0.00157 (    3)
  SS BOND              : angle       0.96671 (    6)
  hydrogen bonds       : bond        0.04286 (  426)
  hydrogen bonds       : angle       4.29654 ( 1248)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: P   27 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.6801 (mp0)
REVERT: R  221 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8554 (tp40)
REVERT: A   17 LYS cc_start: 0.5489 (OUTLIER) cc_final: 0.4363 (ptpt)
REVERT: A  230 ARG cc_start: 0.7376 (mtp-110) cc_final: 0.7114 (ttm110)
REVERT: B  253 PHE cc_start: 0.6643 (m-80) cc_final: 0.6359 (m-80)
  outliers start: 22
  outliers final: 10
  residues processed: 100
  average time/residue: 0.5267
  time to fit residues: 56.1922
Evaluate side-chains
  87 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   27 GLU
Chi-restraints excluded: chain R residue   43 ARG
Chi-restraints excluded: chain R residue  211 GLN
Chi-restraints excluded: chain R residue  221 GLN
Chi-restraints excluded: chain R residue  360 LEU
Chi-restraints excluded: chain R residue  405 VAL
Chi-restraints excluded: chain A residue   17 LYS
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  291 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 89 optimal weight:    5.9990
   chunk 9 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 83 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9990
   chunk 87 optimal weight:    5.9990
   chunk 86 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A  43 ASN
B 155 ASN
G  18 GLN
G  44 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.218703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.163016 restraints weight = 8476.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3899 rms_B_bonded: 2.01
r_work: 0.3480 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.1008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8227  Z= 0.145
  Angle     :  0.507   7.793  11171  Z= 0.272
  Chirality :  0.042   0.142   1254
  Planarity :  0.004   0.057   1412
  Dihedral  :  4.452  57.449   1112
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.41 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 18.40 %
    Favored  : 78.07 %
  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:  1.00 (0.26), residues: 997
  helix:  2.31 (0.24), residues: 432
  sheet: -0.17 (0.38), residues: 181
  loop : -0.83 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  31 
 TYR   0.023   0.002   TYR R 148 
 PHE   0.018   0.002   PHE R 143 
 TRP   0.017   0.002   TRP B 169 
 HIS   0.007   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 8224)
  covalent geometry    : angle       0.50682 (11165)
  SS BOND              : bond        0.00329 (    3)
  SS BOND              : angle       1.04097 (    6)
  hydrogen bonds       : bond        0.04389 (  426)
  hydrogen bonds       : angle       4.21777 ( 1248)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 73
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: P   27 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.6930 (mp0)
REVERT: R  221 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8665 (tp40)
REVERT: A   17 LYS cc_start: 0.6020 (OUTLIER) cc_final: 0.4875 (ptpt)
REVERT: A  187 PHE cc_start: 0.7190 (p90) cc_final: 0.6940 (p90)
REVERT: B   59 TYR cc_start: 0.8095 (OUTLIER) cc_final: 0.7722 (m-80)
REVERT: B  253 PHE cc_start: 0.6964 (m-80) cc_final: 0.6716 (m-80)
  outliers start: 30
  outliers final: 14
  residues processed: 94
  average time/residue: 0.5266
  time to fit residues: 52.7123
Evaluate side-chains
  92 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   27 GLU
Chi-restraints excluded: chain R residue  125 GLU
Chi-restraints excluded: chain R residue  211 GLN
Chi-restraints excluded: chain R residue  221 GLN
Chi-restraints excluded: chain R residue  360 LEU
Chi-restraints excluded: chain R residue  405 VAL
Chi-restraints excluded: chain A residue   17 LYS
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   43 ASN
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  291 ASP
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  321 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 6 optimal weight:   20.0000
   chunk 79 optimal weight:    8.9990
   chunk 28 optimal weight:    0.0270
   chunk 65 optimal weight:    0.0670
   chunk 92 optimal weight:    7.9990
   chunk 18 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 88 optimal weight:    0.2980
   chunk 7 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.4176

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

Flipped N/Q/H residues before XYZ refinement:
G  44 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.220307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.157175 restraints weight = 8716.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.3690 rms_B_bonded: 2.16
r_work: 0.3333 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3189 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.1181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8227  Z= 0.105
  Angle     :  0.475   7.933  11171  Z= 0.253
  Chirality :  0.040   0.139   1254
  Planarity :  0.004   0.050   1412
  Dihedral  :  4.357  58.099   1112
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.31 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 18.28 %
    Favored  : 78.30 %
  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:  1.14 (0.27), residues: 997
  helix:  2.45 (0.24), residues: 433
  sheet: -0.11 (0.38), residues: 181
  loop : -0.81 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 230 
 TYR   0.020   0.001   TYR R 148 
 PHE   0.017   0.001   PHE R 230 
 TRP   0.015   0.001   TRP R  33 
 HIS   0.006   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 8224)
  covalent geometry    : angle       0.47446 (11165)
  SS BOND              : bond        0.00180 (    3)
  SS BOND              : angle       0.92001 (    6)
  hydrogen bonds       : bond        0.03884 (  426)
  hydrogen bonds       : angle       4.01031 ( 1248)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 77
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: P   27 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.6888 (mp0)
REVERT: R  334 LYS cc_start: 0.7297 (OUTLIER) cc_final: 0.6772 (mmmt)
REVERT: A   17 LYS cc_start: 0.5509 (OUTLIER) cc_final: 0.4413 (ptpt)
REVERT: A  187 PHE cc_start: 0.7050 (p90) cc_final: 0.6716 (p90)
REVERT: B   59 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.7907 (m-80)
  outliers start: 29
  outliers final: 14
  residues processed: 96
  average time/residue: 0.4843
  time to fit residues: 49.9253
Evaluate side-chains
  91 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   27 GLU
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  125 GLU
Chi-restraints excluded: chain R residue  211 GLN
Chi-restraints excluded: chain R residue  334 LYS
Chi-restraints excluded: chain R residue  360 LEU
Chi-restraints excluded: chain R residue  405 VAL
Chi-restraints excluded: chain A residue   17 LYS
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  291 ASP
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain G residue   21 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 94 optimal weight:    3.9990
   chunk 73 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 30 optimal weight:    0.5980
   chunk 52 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 214 ASN
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  44 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.219291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.163705 restraints weight = 8610.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.3868 rms_B_bonded: 2.02
r_work: 0.3448 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3296 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.1277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8227  Z= 0.136
  Angle     :  0.502  10.469  11171  Z= 0.265
  Chirality :  0.041   0.142   1254
  Planarity :  0.004   0.055   1412
  Dihedral  :  4.398  55.961   1112
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.61 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 18.87 %
    Favored  : 77.59 %
  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:  1.01 (0.26), residues: 997
  helix:  2.31 (0.24), residues: 433
  sheet: -0.20 (0.39), residues: 182
  loop : -0.81 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 380 
 TYR   0.022   0.001   TYR R 148 
 PHE   0.016   0.001   PHE R 230 
 TRP   0.016   0.001   TRP R  33 
 HIS   0.006   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8224)
  covalent geometry    : angle       0.50143 (11165)
  SS BOND              : bond        0.00315 (    3)
  SS BOND              : angle       1.00662 (    6)
  hydrogen bonds       : bond        0.04145 (  426)
  hydrogen bonds       : angle       4.05854 ( 1248)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 74
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: P   27 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7430 (mp0)
REVERT: A   17 LYS cc_start: 0.5772 (OUTLIER) cc_final: 0.4646 (ptpt)
REVERT: B   59 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.7980 (m-80)
  outliers start: 30
  outliers final: 16
  residues processed: 94
  average time/residue: 0.4781
  time to fit residues: 48.1453
Evaluate side-chains
  93 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   27 GLU
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  125 GLU
Chi-restraints excluded: chain R residue  211 GLN
Chi-restraints excluded: chain R residue  360 LEU
Chi-restraints excluded: chain R residue  405 VAL
Chi-restraints excluded: chain A residue   17 LYS
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain G residue   21 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0570
   chunk 11 optimal weight:    8.9990
   chunk 88 optimal weight:    4.9990
   chunk 55 optimal weight:   10.0000
   chunk 91 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.7100

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

Flipped N/Q/H residues before XYZ refinement:
R  37 GLN
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  44 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.218965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 112)---------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.138289 restraints weight = 8631.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 2.44
r_work: 0.3356 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7270
moved from start:          0.1384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8227  Z= 0.125
  Angle     :  0.491   9.083  11171  Z= 0.260
  Chirality :  0.041   0.149   1254
  Planarity :  0.004   0.054   1412
  Dihedral  :  4.360  55.890   1112
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.41 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 18.75 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.27), residues: 997
  helix:  2.29 (0.24), residues: 440
  sheet: -0.15 (0.39), residues: 181
  loop : -0.81 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 230 
 TYR   0.021   0.001   TYR R 148 
 PHE   0.017   0.001   PHE R 230 
 TRP   0.017   0.001   TRP R  33 
 HIS   0.007   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8224)
  covalent geometry    : angle       0.49019 (11165)
  SS BOND              : bond        0.00246 (    3)
  SS BOND              : angle       0.94814 (    6)
  hydrogen bonds       : bond        0.03997 (  426)
  hydrogen bonds       : angle       3.98651 ( 1248)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 74
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  334 LYS cc_start: 0.7268 (OUTLIER) cc_final: 0.6686 (mmmt)
REVERT: A   17 LYS cc_start: 0.5433 (OUTLIER) cc_final: 0.4405 (ptpt)
REVERT: A  196 MET cc_start: 0.7577 (ttp) cc_final: 0.7352 (ttp)
REVERT: B   59 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.7643 (m-80)
  outliers start: 33
  outliers final: 19
  residues processed: 95
  average time/residue: 0.5066
  time to fit residues: 51.3939
Evaluate side-chains
  96 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 74
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   27 GLU
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  125 GLU
Chi-restraints excluded: chain R residue  211 GLN
Chi-restraints excluded: chain R residue  301 SER
Chi-restraints excluded: chain R residue  334 LYS
Chi-restraints excluded: chain R residue  360 LEU
Chi-restraints excluded: chain R residue  405 VAL
Chi-restraints excluded: chain A residue   17 LYS
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  291 ASP
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   21 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0980
   chunk 91 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 97 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 50 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 82 optimal weight:   10.0000
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
R  37 GLN
A 195 HIS
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  44 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.218797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 100)---------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.136831 restraints weight = 8664.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 2.50
r_work: 0.3339 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7271
moved from start:          0.1422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8227  Z= 0.128
  Angle     :  0.493   8.634  11171  Z= 0.261
  Chirality :  0.041   0.145   1254
  Planarity :  0.004   0.056   1412
  Dihedral  :  4.363  55.601   1112
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.41 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 18.63 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.03 (0.27), residues: 997
  helix:  2.28 (0.24), residues: 441
  sheet: -0.18 (0.38), residues: 181
  loop : -0.80 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 230 
 TYR   0.021   0.001   TYR R 148 
 PHE   0.016   0.001   PHE R 230 
 TRP   0.019   0.001   TRP R  33 
 HIS   0.006   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8224)
  covalent geometry    : angle       0.49301 (11165)
  SS BOND              : bond        0.00246 (    3)
  SS BOND              : angle       0.93471 (    6)
  hydrogen bonds       : bond        0.04012 (  426)
  hydrogen bonds       : angle       3.96647 ( 1248)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 76
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  334 LYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6569 (mmtt)
REVERT: A   17 LYS cc_start: 0.5377 (OUTLIER) cc_final: 0.4364 (ptpt)
REVERT: A  196 MET cc_start: 0.7497 (ttp) cc_final: 0.7261 (ttp)
REVERT: B   59 TYR cc_start: 0.8106 (OUTLIER) cc_final: 0.7670 (m-80)
  outliers start: 34
  outliers final: 20
  residues processed: 101
  average time/residue: 0.4951
  time to fit residues: 53.4161
Evaluate side-chains
  99 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 76
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   27 GLU
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  111 LEU
Chi-restraints excluded: chain R residue  125 GLU
Chi-restraints excluded: chain R residue  211 GLN
Chi-restraints excluded: chain R residue  301 SER
Chi-restraints excluded: chain R residue  334 LYS
Chi-restraints excluded: chain R residue  360 LEU
Chi-restraints excluded: chain R residue  405 VAL
Chi-restraints excluded: chain A residue   17 LYS
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  291 ASP
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain G residue   21 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    5.9990
   chunk 38 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 62 optimal weight:    0.3980
   chunk 37 optimal weight:    0.5980
   chunk 86 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 119 ASN
G  44 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.218703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.136157 restraints weight = 8663.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 2.33
r_work: 0.3346 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
moved from start:          0.1522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8227  Z= 0.117
  Angle     :  0.491   8.577  11171  Z= 0.259
  Chirality :  0.041   0.146   1254
  Planarity :  0.004   0.053   1412
  Dihedral  :  4.328  55.483   1112
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.41 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 19.69 %
    Favored  : 77.24 %
  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:  1.10 (0.27), residues: 997
  helix:  2.35 (0.24), residues: 441
  sheet: -0.18 (0.39), residues: 179
  loop : -0.77 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 230 
 TYR   0.020   0.001   TYR R 148 
 PHE   0.018   0.001   PHE R 230 
 TRP   0.026   0.001   TRP R  33 
 HIS   0.007   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 8224)
  covalent geometry    : angle       0.49057 (11165)
  SS BOND              : bond        0.00220 (    3)
  SS BOND              : angle       0.89150 (    6)
  hydrogen bonds       : bond        0.03867 (  426)
  hydrogen bonds       : angle       3.91080 ( 1248)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 78
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  334 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6562 (mmmt)
REVERT: A   17 LYS cc_start: 0.5398 (OUTLIER) cc_final: 0.4387 (ptpt)
REVERT: A  196 MET cc_start: 0.7421 (ttp) cc_final: 0.7195 (ttp)
REVERT: B   59 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.7973 (m-80)
  outliers start: 26
  outliers final: 20
  residues processed: 97
  average time/residue: 0.4907
  time to fit residues: 50.7965
Evaluate side-chains
  99 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 76
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   27 GLU
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  111 LEU
Chi-restraints excluded: chain R residue  125 GLU
Chi-restraints excluded: chain R residue  211 GLN
Chi-restraints excluded: chain R residue  301 SER
Chi-restraints excluded: chain R residue  334 LYS
Chi-restraints excluded: chain R residue  360 LEU
Chi-restraints excluded: chain R residue  405 VAL
Chi-restraints excluded: chain A residue   17 LYS
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  291 ASP
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain G residue   21 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 96 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 77 optimal weight:    5.9990
   chunk 30 optimal weight:    0.3980
   chunk 57 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 73 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   chunk 97 optimal weight:    7.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
R  37 GLN
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  44 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.217534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 104)---------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.137970 restraints weight = 8587.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 2.07
r_work: 0.3203 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.3047 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.1563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8227  Z= 0.151
  Angle     :  0.525   9.386  11171  Z= 0.277
  Chirality :  0.042   0.145   1254
  Planarity :  0.004   0.059   1412
  Dihedral  :  4.467  54.441   1112
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.71 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 19.58 %
    Favored  : 77.12 %
  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:  0.99 (0.27), residues: 997
  helix:  2.29 (0.24), residues: 434
  sheet: -0.27 (0.39), residues: 179
  loop : -0.78 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 230 
 TYR   0.022   0.002   TYR R 148 
 PHE   0.019   0.002   PHE R 230 
 TRP   0.032   0.002   TRP R  33 
 HIS   0.007   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 8224)
  covalent geometry    : angle       0.52433 (11165)
  SS BOND              : bond        0.00339 (    3)
  SS BOND              : angle       0.95349 (    6)
  hydrogen bonds       : bond        0.04266 (  426)
  hydrogen bonds       : angle       4.01777 ( 1248)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 80
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  334 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6731 (mmtt)
REVERT: A   17 LYS cc_start: 0.5301 (OUTLIER) cc_final: 0.4271 (ptpt)
REVERT: B   59 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.7938 (m-80)
  outliers start: 28
  outliers final: 20
  residues processed: 99
  average time/residue: 0.5077
  time to fit residues: 53.6656
Evaluate side-chains
  101 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 78
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   27 GLU
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  111 LEU
Chi-restraints excluded: chain R residue  125 GLU
Chi-restraints excluded: chain R residue  211 GLN
Chi-restraints excluded: chain R residue  301 SER
Chi-restraints excluded: chain R residue  334 LYS
Chi-restraints excluded: chain R residue  360 LEU
Chi-restraints excluded: chain R residue  405 VAL
Chi-restraints excluded: chain A residue   17 LYS
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  291 ASP
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain G residue   21 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 72 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 87 optimal weight:    0.0030
   chunk 28 optimal weight:    0.6980
   chunk 12 optimal weight:    9.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.6392

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

Flipped N/Q/H residues before XYZ refinement:
R  37 GLN
A 195 HIS
A 214 ASN
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  44 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.218216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.139749 restraints weight = 8581.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 2.61
r_work: 0.3327 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7273
moved from start:          0.1638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8227  Z= 0.121
  Angle     :  0.501   9.359  11171  Z= 0.265
  Chirality :  0.041   0.145   1254
  Planarity :  0.004   0.057   1412
  Dihedral  :  4.374  54.585   1112
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.41 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 19.46 %
    Favored  : 77.24 %
  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:  1.15 (0.27), residues: 997
  helix:  2.42 (0.24), residues: 434
  sheet: -0.14 (0.38), residues: 179
  loop : -0.73 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 230 
 TYR   0.020   0.001   TYR R 148 
 PHE   0.019   0.001   PHE R 230 
 TRP   0.037   0.001   TRP R  33 
 HIS   0.006   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 8224)
  covalent geometry    : angle       0.50121 (11165)
  SS BOND              : bond        0.00201 (    3)
  SS BOND              : angle       0.85988 (    6)
  hydrogen bonds       : bond        0.03920 (  426)
  hydrogen bonds       : angle       3.90923 ( 1248)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 73
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  292 GLU cc_start: 0.7935 (tt0) cc_final: 0.7727 (tt0)
REVERT: R  334 LYS cc_start: 0.7253 (OUTLIER) cc_final: 0.6734 (mmtt)
REVERT: A   17 LYS cc_start: 0.5388 (OUTLIER) cc_final: 0.4334 (ptpt)
REVERT: B   59 TYR cc_start: 0.8112 (OUTLIER) cc_final: 0.7757 (m-80)
  outliers start: 28
  outliers final: 20
  residues processed: 92
  average time/residue: 0.5182
  time to fit residues: 50.8358
Evaluate side-chains
  96 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 73
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   27 GLU
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  111 LEU
Chi-restraints excluded: chain R residue  125 GLU
Chi-restraints excluded: chain R residue  211 GLN
Chi-restraints excluded: chain R residue  301 SER
Chi-restraints excluded: chain R residue  334 LYS
Chi-restraints excluded: chain R residue  360 LEU
Chi-restraints excluded: chain R residue  405 VAL
Chi-restraints excluded: chain A residue   17 LYS
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  291 ASP
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain G residue   21 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 45 optimal weight:    7.9990
   chunk 80 optimal weight:    0.9990
   chunk 85 optimal weight:    0.4980
   chunk 1 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0050
   chunk 47 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   chunk 48 optimal weight:    0.4980
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  44 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.226625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 108)---------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.157456 restraints weight = 8456.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 2.48
r_work: 0.3280 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7336
moved from start:          0.1652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8227  Z= 0.118
  Angle     :  0.498   9.320  11171  Z= 0.262
  Chirality :  0.041   0.146   1254
  Planarity :  0.004   0.055   1412
  Dihedral  :  4.349  54.368   1112
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.71 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 20.40 %
    Favored  : 76.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.27), residues: 997
  helix:  2.44 (0.24), residues: 434
  sheet: -0.25 (0.38), residues: 181
  loop : -0.75 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 230 
 TYR   0.020   0.001   TYR R 148 
 PHE   0.020   0.001   PHE R 230 
 TRP   0.033   0.001   TRP R  33 
 HIS   0.007   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 8224)
  covalent geometry    : angle       0.49794 (11165)
  SS BOND              : bond        0.00216 (    3)
  SS BOND              : angle       0.90461 (    6)
  hydrogen bonds       : bond        0.03846 (  426)
  hydrogen bonds       : angle       3.87784 ( 1248)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3338.92 seconds
wall clock time: 57 minutes 23.82 seconds (3443.82 seconds total)