Starting phenix.real_space_refine
on Wed Feb  4 05:20:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9p92_71396/02_2026/9p92_71396.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9p92_71396/02_2026/9p92_71396.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9p92_71396/02_2026/9p92_71396.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9p92_71396/02_2026/9p92_71396.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9p92_71396/02_2026/9p92_71396.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9p92_71396/02_2026/9p92_71396.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.003 sd=   0.037
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      57      5.16       5
     C    5544      2.51       5
     N    1535      2.21       5
     O    1622      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8758
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1886
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1886
          Classifications: {'peptide': 226}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 219}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 2601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2601
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 424
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "R"
      Number of atoms: 2652
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 358, 2652
          Classifications: {'peptide': 358}
          Incomplete info: {'truncation_to_alanine': 80}
          Link IDs: {'PTRANS': 12, 'TRANS': 345}
          Chain breaks: 4
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 306
          Unresolved non-hydrogen angles: 396
          Unresolved non-hydrogen dihedrals: 268
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'PHE:plan': 6, 'GLU:plan': 9, 'GLN:plan1': 3, 'ARG:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 4, 'ASP:plan': 7, 'HIS:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 185
    Chain: "P"
      Number of atoms: 234
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 234
          Classifications: {'peptide': 28}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 27}
  Time building chain proxies: 2.30, per 1000 atoms: 0.26
  Number of scatterers: 8758
  At special positions: 0
  Unit cell: (78.26, 101.48, 167.7, 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      57     16.00
     O    1622      8.00
     N    1535      7.00
     C    5544      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  34 " - pdb=" SG  CYS R  63 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  54 " - pdb=" SG  CYS R 118 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  77 " - pdb=" SG  CYS R 134 " 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: 0.73
  Conformation dependent library (CDL) restraints added in 358.1 milliseconds
  

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2126

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 11 sheets defined
      42.9% alpha, 19.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 40
      removed outlier: 3.933A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   ASP A  33 " --> pdb=" O   GLN A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 61
    Processing helix  chain 'A' and resid 233 through 239
    Processing helix  chain 'A' and resid 264 through 279
    Processing helix  chain 'A' and resid 281 through 285
      removed outlier: 3.856A  pdb=" N   ASP A 284 " --> pdb=" O   TRP A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 302
    Processing helix  chain 'A' and resid 312 through 317
    Processing helix  chain 'A' and resid 331 through 351
    Processing helix  chain 'A' and resid 370 through 392
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 9 through 24
    Processing helix  chain 'G' and resid 29 through 45
      removed outlier: 3.520A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 74 through 76
      No H-bonds generated for 'chain 'N' and resid 74 through 76'
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 25 through 33
      removed outlier: 3.713A  pdb=" N   LYS R  29 " --> pdb=" O   CYS R  25 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 33 through 42
      removed outlier: 4.406A  pdb=" N   LYS R  37 " --> pdb=" O   MET R  33 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ALA R  41 " --> pdb=" O   LYS R  37 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 79 through 83
      removed outlier: 3.838A  pdb=" N   ILE R  83 " --> pdb=" O   LEU R  80 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 129 through 134
    Processing helix  chain 'R' and resid 146 through 177
      removed outlier: 3.570A  pdb=" N   ARG R 177 " --> pdb=" O   VAL R 173 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 183 through 212
      removed outlier: 3.860A  pdb=" N   LEU R 192 " --> pdb=" O   ILE R 188 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 223 through 257
      removed outlier: 3.858A  pdb=" N   LYS R 227 " --> pdb=" O   THR R 223 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   PHE R 245 " --> pdb=" O   TYR R 241 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 264 through 291
      Proline residue:  R 277  - end of helix
    Processing helix  chain 'R' and resid 302 through 337
      removed outlier: 3.935A  pdb=" N   VAL R 308 " --> pdb=" O   ALA R 304 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   ILE R 309 " --> pdb=" O   LEU R 305 " (cutoff:3.500A)
      Proline residue:  R 312  - end of helix
      removed outlier: 4.017A  pdb=" N   ILE R 317 " --> pdb=" O   VAL R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 348 through 363
      Proline residue:  R 360  - end of helix
    Processing helix  chain 'R' and resid 366 through 371
      removed outlier: 4.204A  pdb=" N   PHE R 371 " --> pdb=" O   THR R 367 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 379 through 387
      removed outlier: 3.987A  pdb=" N   VAL R 383 " --> pdb=" O   ARG R 379 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   PHE R 384 " --> pdb=" O   GLU R 380 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 388 through 390
      No H-bonds generated for 'chain 'R' and resid 388 through 390'
    Processing helix  chain 'R' and resid 391 through 401
    Processing helix  chain 'R' and resid 406 through 418
    Processing helix  chain 'P' and resid 2 through 28
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 6.705A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.790A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.510A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.660A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52
      removed outlier: 5.725A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 5.450A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.064A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.476A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.511A  pdb=" N   THR B 102 " --> pdb=" O   GLY B 115 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.024A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.805A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.949A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 7.256A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.775A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.591A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.321A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 5.831A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
      removed outlier: 4.001A  pdb=" N   GLN N   3 " --> pdb=" O   SER N  25 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   SER N  25 " --> pdb=" O   GLN N   3 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   THR N  78 " --> pdb=" O   ASP N  73 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ASP N  73 " --> pdb=" O   THR N  78 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11
      removed outlier: 6.419A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 7.678A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 5.112A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 71 through 77
      removed outlier: 3.738A  pdb=" N   GLU R  71 " --> pdb=" O   CYS R 118 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLY R 112 " --> pdb=" O   CYS R  77 " (cutoff:3.500A)

    454 hydrogen bonds defined for protein.
    1281 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: 1.44

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1833
        1.33 -     1.45: 2148
        1.45 -     1.57: 4873
        1.57 -     1.69: 0
        1.69 -     1.82: 78
  Bond restraints: 8932
  Sorted by residual:
  bond pdb=" N   VAL R  75 "
       pdb=" CA  VAL R  75 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.038 1.11e-02 8.12e+03 1.17e+01
  bond pdb=" N   VAL R  73 "
       pdb=" CA  VAL R  73 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.038 1.20e-02 6.94e+03 1.00e+01
  bond pdb=" N   ILE R  95 "
       pdb=" CA  ILE R  95 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.19e-02 7.06e+03 9.55e+00
  bond pdb=" N   ILE R 359 "
       pdb=" CA  ILE R 359 "
    ideal  model  delta    sigma   weight residual
    1.463  1.499 -0.036 1.20e-02 6.94e+03 9.24e+00
  bond pdb=" N   ILE R 330 "
       pdb=" CA  ILE R 330 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.036 1.19e-02 7.06e+03 9.22e+00
  ... (remaining 8927 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 11464
        1.65 -     3.29: 553
        3.29 -     4.94: 79
        4.94 -     6.58: 4
        6.58 -     8.23: 3
  Bond angle restraints: 12103
  Sorted by residual:
  angle pdb=" C   CYS R  77 "
        pdb=" CA  CYS R  77 "
        pdb=" CB  CYS R  77 "
      ideal   model   delta    sigma   weight residual
     108.63  114.63   -6.00 1.54e+00 4.22e-01 1.52e+01
  angle pdb=" CA  CYS R 183 "
        pdb=" C   CYS R 183 "
        pdb=" O   CYS R 183 "
      ideal   model   delta    sigma   weight residual
     121.31  117.18    4.13 1.07e+00 8.73e-01 1.49e+01
  angle pdb=" O   THR R 258 "
        pdb=" C   THR R 258 "
        pdb=" N   PHE R 259 "
      ideal   model   delta    sigma   weight residual
     122.07  126.02   -3.95 1.03e+00 9.43e-01 1.47e+01
  angle pdb=" CA  ILE R 359 "
        pdb=" C   ILE R 359 "
        pdb=" N   PRO R 360 "
      ideal   model   delta    sigma   weight residual
     120.83  123.15   -2.32 6.10e-01 2.69e+00 1.44e+01
  angle pdb=" N   ASP R 102 "
        pdb=" CA  ASP R 102 "
        pdb=" C   ASP R 102 "
      ideal   model   delta    sigma   weight residual
     111.28  107.15    4.13 1.09e+00 8.42e-01 1.43e+01
  ... (remaining 12098 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 4868
       17.95 -    35.90: 363
       35.90 -    53.85: 49
       53.85 -    71.80: 9
       71.80 -    89.75: 6
  Dihedral angle restraints: 5295
    sinusoidal: 2011
      harmonic: 3284
  Sorted by residual:
  dihedral pdb=" CB  CYS R  77 "
           pdb=" SG  CYS R  77 "
           pdb=" SG  CYS R 134 "
           pdb=" CB  CYS R 134 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  146.57  -53.57     1      1.00e+01 1.00e-02 3.90e+01
  dihedral pdb=" CG  ARG N  67 "
           pdb=" CD  ARG N  67 "
           pdb=" NE  ARG N  67 "
           pdb=" CZ  ARG N  67 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.81   44.19     2      1.50e+01 4.44e-03 1.04e+01
  dihedral pdb=" CA  ALA B  56 "
           pdb=" C   ALA B  56 "
           pdb=" N   LYS B  57 "
           pdb=" CA  LYS B  57 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.92   16.08     0      5.00e+00 4.00e-02 1.03e+01
  ... (remaining 5292 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1098
       0.057 -    0.115: 190
       0.115 -    0.172: 58
       0.172 -    0.229: 12
       0.229 -    0.287: 2
  Chirality restraints: 1360
  Sorted by residual:
  chirality pdb=" CA  PHE R 100 "
            pdb=" N   PHE R 100 "
            pdb=" C   PHE R 100 "
            pdb=" CB  PHE R 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.06e+00
  chirality pdb=" CA  LYS R 206 "
            pdb=" N   LYS R 206 "
            pdb=" C   LYS R 206 "
            pdb=" CB  LYS R 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" CA  LEU R  74 "
            pdb=" N   LEU R  74 "
            pdb=" C   LEU R  74 "
            pdb=" CB  LEU R  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.31e+00
  ... (remaining 1357 not shown)

  Planarity restraints: 1550
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 311 "   -0.039 5.00e-02 4.00e+02   5.87e-02 5.52e+00
        pdb=" N   PRO R 312 "    0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO R 312 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO R 312 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 210 "   -0.011 2.00e-02 2.50e+03   2.26e-02 5.12e+00
        pdb=" C   LEU R 210 "    0.039 2.00e-02 2.50e+03
        pdb=" O   LEU R 210 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   TYR R 211 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE P   6 "    0.009 2.00e-02 2.50e+03   1.79e-02 3.21e+00
        pdb=" C   PHE P   6 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   PHE P   6 "    0.012 2.00e-02 2.50e+03
        pdb=" N   THR P   7 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1547 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2264
        2.80 -     3.33: 8636
        3.33 -     3.85: 14083
        3.85 -     4.38: 15927
        4.38 -     4.90: 27914
  Nonbonded interactions: 68824
  Sorted by model distance:
  nonbonded pdb=" O   ALA B 231 "
            pdb=" OG1 THR B 243 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" O   ASP B 163 "
            pdb=" OG1 THR B 164 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   THR N 113 "
            pdb=" OG1 THR N 114 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" OD1 ASP N  50 "
            pdb=" OG  SER N  59 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" N   GLU N  89 "
            pdb=" OE1 GLU N  89 "
     model   vdw
     2.313 3.120
  ... (remaining 68819 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     10.020
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
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   0.038   8938  Z= 0.338
  Angle     :  0.737   8.230  12115  Z= 0.503
  Chirality :  0.053   0.287   1360
  Planarity :  0.004   0.059   1550
  Dihedral  : 12.707  89.754   3151
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  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:  0.84 (0.26), residues: 1103
  helix:  1.48 (0.26), residues: 425
  sheet:  0.73 (0.34), residues: 224
  loop : -0.35 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  27 
 TYR   0.023   0.001   TYR R 157 
 PHE   0.016   0.001   PHE R 232 
 TRP   0.018   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 8932)
  covalent geometry    : angle       0.73698 (12103)
  SS BOND              : bond        0.00156 (    6)
  SS BOND              : angle       0.79048 (   12)
  hydrogen bonds       : bond        0.18263 (  454)
  hydrogen bonds       : angle       6.47201 ( 1281)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  360 TYR cc_start: 0.8595 (m-80) cc_final: 0.8357 (m-80)
REVERT: B  260 GLU cc_start: 0.7514 (tt0) cc_final: 0.7312 (tt0)
REVERT: G   16 VAL cc_start: 0.9014 (p) cc_final: 0.8775 (p)
REVERT: N   47 TRP cc_start: 0.8224 (t60) cc_final: 0.7751 (t60)
REVERT: N   80 TYR cc_start: 0.7647 (m-80) cc_final: 0.7377 (m-10)
REVERT: R   87 ASP cc_start: 0.7904 (m-30) cc_final: 0.7085 (t70)
REVERT: R  293 ASP cc_start: 0.7707 (m-30) cc_final: 0.7306 (t0)
REVERT: R  378 LYS cc_start: 0.8747 (mttt) cc_final: 0.8521 (mtmt)
REVERT: P   15 LYS cc_start: 0.9082 (ttmm) cc_final: 0.8680 (ttpp)
  outliers start: 0
  outliers final: 0
  residues processed: 229
  average time/residue: 0.1300
  time to fit residues: 38.5384
Evaluate side-chains
  152 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    0.0050
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:    0.9990
   overall best weight:    0.8998

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

Flipped N/Q/H residues before XYZ refinement:
N  13 GLN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 186 ASN
R 191 ASN
** P  16 GLN ** 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 = 0.3844 r_free = 0.3844 target = 0.119742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.093378 restraints weight = 21165.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.096244 restraints weight = 12033.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.098179 restraints weight = 8444.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.099485 restraints weight = 6690.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.100247 restraints weight = 5707.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8938  Z= 0.133
  Angle     :  0.585  10.261  12115  Z= 0.312
  Chirality :  0.042   0.159   1360
  Planarity :  0.004   0.046   1550
  Dihedral  :  4.259  45.457   1229
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  9.86 %
    Favored  : 88.70 %
  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:  0.96 (0.26), residues: 1103
  helix:  1.53 (0.24), residues: 444
  sheet:  0.77 (0.34), residues: 228
  loop : -0.31 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG P  12 
 TYR   0.022   0.001   TYR R 157 
 PHE   0.029   0.001   PHE R 260 
 TRP   0.017   0.001   TRP R 274 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 8932)
  covalent geometry    : angle       0.58478 (12103)
  SS BOND              : bond        0.00386 (    6)
  SS BOND              : angle       0.61382 (   12)
  hydrogen bonds       : bond        0.04512 (  454)
  hydrogen bonds       : angle       4.87583 ( 1281)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 174
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  360 TYR cc_start: 0.8491 (m-80) cc_final: 0.8158 (m-80)
REVERT: B   52 ARG cc_start: 0.8123 (mtt-85) cc_final: 0.7641 (mtt-85)
REVERT: B   89 LYS cc_start: 0.7830 (ptpt) cc_final: 0.7282 (ptmt)
REVERT: B  260 GLU cc_start: 0.7818 (tt0) cc_final: 0.7562 (tt0)
REVERT: G   36 ASP cc_start: 0.8396 (t0) cc_final: 0.7745 (m-30)
REVERT: G   42 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8116 (mm-30)
REVERT: N   13 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.6605 (mm-40)
REVERT: N   47 TRP cc_start: 0.8208 (t60) cc_final: 0.7781 (t60)
REVERT: R   87 ASP cc_start: 0.7902 (m-30) cc_final: 0.7178 (t70)
REVERT: R  269 TYR cc_start: 0.8705 (m-10) cc_final: 0.8445 (m-80)
REVERT: R  293 ASP cc_start: 0.7919 (m-30) cc_final: 0.7400 (t0)
REVERT: R  305 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8160 (mm)
REVERT: R  318 MET cc_start: 0.7634 (mmp) cc_final: 0.7430 (mmt)
REVERT: R  378 LYS cc_start: 0.8756 (mttt) cc_final: 0.8543 (mtpp)
REVERT: P   15 LYS cc_start: 0.9077 (ttmm) cc_final: 0.8712 (ttpt)
  outliers start: 13
  outliers final: 7
  residues processed: 180
  average time/residue: 0.1118
  time to fit residues: 27.0477
Evaluate side-chains
  162 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 153
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   13 GLN
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue  271 ILE
Chi-restraints excluded: chain R residue  305 LEU
Chi-restraints excluded: chain R residue  359 ILE
Chi-restraints excluded: chain P residue    5 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 52 optimal weight:    8.9990
   chunk 45 optimal weight:    4.9990
   chunk 25 optimal weight:    9.9990
   chunk 26 optimal weight:    4.9990
   chunk 42 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   chunk 13 optimal weight:   10.0000
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
P  16 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.114230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.087390 restraints weight = 21267.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.090001 restraints weight = 12296.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.091923 restraints weight = 8791.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.093192 restraints weight = 7008.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.093838 restraints weight = 6024.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.2712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   8938  Z= 0.214
  Angle     :  0.631   7.977  12115  Z= 0.340
  Chirality :  0.043   0.165   1360
  Planarity :  0.004   0.046   1550
  Dihedral  :  4.511  38.656   1229
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 12.74 %
    Favored  : 84.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.25), residues: 1103
  helix:  1.57 (0.24), residues: 440
  sheet:  0.38 (0.33), residues: 232
  loop : -0.39 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG G  13 
 TYR   0.019   0.002   TYR R 400 
 PHE   0.019   0.002   PHE B 151 
 TRP   0.012   0.002   TRP A 234 
 HIS   0.009   0.002   HIS R 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 8932)
  covalent geometry    : angle       0.62881 (12103)
  SS BOND              : bond        0.00423 (    6)
  SS BOND              : angle       1.68170 (   12)
  hydrogen bonds       : bond        0.04736 (  454)
  hydrogen bonds       : angle       4.84071 ( 1281)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 165
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.7756 (mpp) cc_final: 0.7547 (mpp)
REVERT: A  360 TYR cc_start: 0.8763 (m-80) cc_final: 0.8228 (m-80)
REVERT: B    5 ASP cc_start: 0.9155 (m-30) cc_final: 0.8940 (p0)
REVERT: B   52 ARG cc_start: 0.8268 (mtt-85) cc_final: 0.7217 (mtt-85)
REVERT: B  217 MET cc_start: 0.8316 (pmm) cc_final: 0.8060 (pmm)
REVERT: B  260 GLU cc_start: 0.7977 (tt0) cc_final: 0.7709 (tt0)
REVERT: B  335 PHE cc_start: 0.8131 (m-80) cc_final: 0.7515 (m-80)
REVERT: G    9 ILE cc_start: 0.8797 (mm) cc_final: 0.8440 (mm)
REVERT: G   32 LYS cc_start: 0.9084 (mmmm) cc_final: 0.8853 (mmmt)
REVERT: G   36 ASP cc_start: 0.8484 (t0) cc_final: 0.7928 (m-30)
REVERT: N   47 TRP cc_start: 0.8254 (t60) cc_final: 0.7857 (t60)
REVERT: R   87 ASP cc_start: 0.8045 (m-30) cc_final: 0.7294 (t70)
REVERT: R  305 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8314 (mm)
REVERT: R  378 LYS cc_start: 0.8930 (mttt) cc_final: 0.8670 (mtpp)
REVERT: P   15 LYS cc_start: 0.9085 (ttmm) cc_final: 0.8724 (ttpt)
  outliers start: 23
  outliers final: 19
  residues processed: 178
  average time/residue: 0.1124
  time to fit residues: 26.8299
Evaluate side-chains
  168 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   13 GLN
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain R residue  255 LEU
Chi-restraints excluded: chain R residue  263 ARG
Chi-restraints excluded: chain R residue  271 ILE
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  286 THR
Chi-restraints excluded: chain R residue  305 LEU
Chi-restraints excluded: chain R residue  332 VAL
Chi-restraints excluded: chain R residue  357 LEU
Chi-restraints excluded: chain R residue  359 ILE
Chi-restraints excluded: chain P residue    5 VAL
Chi-restraints excluded: chain P residue    7 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 85 optimal weight:    0.5980
   chunk 88 optimal weight:    2.9990
   chunk 82 optimal weight:    5.9990
   chunk 80 optimal weight:   30.0000
   chunk 13 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 46 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 106 optimal weight:    6.9990
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
N  13 GLN
N  31 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.112722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.085976 restraints weight = 21540.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.088727 restraints weight = 12431.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.090575 restraints weight = 8768.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.091817 restraints weight = 7005.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.092529 restraints weight = 6028.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.3262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   8938  Z= 0.202
  Angle     :  0.617  11.394  12115  Z= 0.326
  Chirality :  0.043   0.197   1360
  Planarity :  0.004   0.051   1550
  Dihedral  :  4.501  30.809   1229
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 15.95 %
    Favored  : 81.17 %
  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:  0.65 (0.25), residues: 1103
  helix:  1.55 (0.24), residues: 435
  sheet:  0.16 (0.33), residues: 229
  loop : -0.48 (0.31), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  22 
 TYR   0.017   0.002   TYR R 400 
 PHE   0.018   0.002   PHE B 151 
 TRP   0.018   0.002   TRP R 274 
 HIS   0.006   0.002   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 8932)
  covalent geometry    : angle       0.61657 (12103)
  SS BOND              : bond        0.00417 (    6)
  SS BOND              : angle       0.71510 (   12)
  hydrogen bonds       : bond        0.04587 (  454)
  hydrogen bonds       : angle       4.72593 ( 1281)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 159
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  360 TYR cc_start: 0.8813 (m-80) cc_final: 0.8281 (m-80)
REVERT: A  389 ARG cc_start: 0.8181 (mtt180) cc_final: 0.7897 (mtt180)
REVERT: B   15 LYS cc_start: 0.9167 (tppt) cc_final: 0.8956 (mmmt)
REVERT: B   31 SER cc_start: 0.8968 (m) cc_final: 0.8725 (p)
REVERT: B  111 TYR cc_start: 0.7697 (m-80) cc_final: 0.7425 (m-80)
REVERT: B  260 GLU cc_start: 0.8084 (tt0) cc_final: 0.7841 (tt0)
REVERT: B  268 ASN cc_start: 0.7989 (t0) cc_final: 0.7787 (t0)
REVERT: B  335 PHE cc_start: 0.8266 (m-80) cc_final: 0.7991 (m-80)
REVERT: N   13 GLN cc_start: 0.7092 (OUTLIER) cc_final: 0.6786 (mm-40)
REVERT: N   47 TRP cc_start: 0.8216 (t60) cc_final: 0.7770 (t60)
REVERT: R   87 ASP cc_start: 0.8170 (m-30) cc_final: 0.7420 (t70)
REVERT: R  255 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7794 (mp)
REVERT: R  269 TYR cc_start: 0.8743 (m-10) cc_final: 0.8417 (m-80)
REVERT: R  305 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8313 (mm)
REVERT: R  378 LYS cc_start: 0.8871 (mttt) cc_final: 0.8668 (mtpp)
REVERT: P   15 LYS cc_start: 0.9087 (ttmm) cc_final: 0.8738 (ttpt)
  outliers start: 26
  outliers final: 19
  residues processed: 172
  average time/residue: 0.1129
  time to fit residues: 25.9419
Evaluate side-chains
  164 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 142
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   13 GLN
Chi-restraints excluded: chain N residue   60 TYR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  255 LEU
Chi-restraints excluded: chain R residue  263 ARG
Chi-restraints excluded: chain R residue  271 ILE
Chi-restraints excluded: chain R residue  286 THR
Chi-restraints excluded: chain R residue  305 LEU
Chi-restraints excluded: chain R residue  359 ILE
Chi-restraints excluded: chain P residue    5 VAL
Chi-restraints excluded: chain P residue    7 THR
Chi-restraints excluded: chain P residue   28 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 102 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 87 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 39 optimal weight:    0.2980
   chunk 53 optimal weight:    4.9990
   chunk 77 optimal weight:   30.0000
   chunk 1 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0470
   chunk 74 optimal weight:   40.0000
   overall best weight:    0.8682

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
** N  13 GLN ** 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 = 0.3772 r_free = 0.3772 target = 0.114447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.087969 restraints weight = 21252.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.090780 restraints weight = 12217.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.092717 restraints weight = 8577.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.093877 restraints weight = 6783.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.094832 restraints weight = 5835.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.3329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8938  Z= 0.126
  Angle     :  0.578   9.187  12115  Z= 0.305
  Chirality :  0.041   0.152   1360
  Planarity :  0.003   0.050   1550
  Dihedral  :  4.227  30.144   1229
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 17.39 %
    Favored  : 80.40 %
  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 (0.26), residues: 1103
  helix:  1.69 (0.25), residues: 434
  sheet:  0.14 (0.33), residues: 230
  loop : -0.38 (0.31), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 356 
 TYR   0.018   0.001   TYR R 157 
 PHE   0.028   0.001   PHE R 178 
 TRP   0.009   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8932)
  covalent geometry    : angle       0.57828 (12103)
  SS BOND              : bond        0.00280 (    6)
  SS BOND              : angle       0.43751 (   12)
  hydrogen bonds       : bond        0.03979 (  454)
  hydrogen bonds       : angle       4.50567 ( 1281)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 153
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  360 TYR cc_start: 0.8788 (m-80) cc_final: 0.8240 (m-80)
REVERT: A  391 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.7263 (t80)
REVERT: B   61 MET cc_start: 0.7994 (ppp) cc_final: 0.7740 (ptm)
REVERT: B  260 GLU cc_start: 0.8085 (tt0) cc_final: 0.7855 (tt0)
REVERT: B  268 ASN cc_start: 0.7941 (t0) cc_final: 0.7722 (t0)
REVERT: G   20 LYS cc_start: 0.9297 (mtmm) cc_final: 0.8732 (mtmm)
REVERT: G   32 LYS cc_start: 0.9131 (mmmm) cc_final: 0.8923 (mmmt)
REVERT: N   13 GLN cc_start: 0.7039 (OUTLIER) cc_final: 0.6713 (mm-40)
REVERT: N   47 TRP cc_start: 0.8188 (t60) cc_final: 0.7695 (t60)
REVERT: R   87 ASP cc_start: 0.8133 (m-30) cc_final: 0.7375 (t70)
REVERT: R  269 TYR cc_start: 0.8745 (m-10) cc_final: 0.8454 (m-80)
REVERT: R  305 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8348 (mm)
REVERT: P   15 LYS cc_start: 0.9071 (ttmm) cc_final: 0.8717 (ttpt)
  outliers start: 20
  outliers final: 12
  residues processed: 163
  average time/residue: 0.1089
  time to fit residues: 24.0599
Evaluate side-chains
  156 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 141
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ASN
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   13 GLN
Chi-restraints excluded: chain N residue   60 TYR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain R residue  271 ILE
Chi-restraints excluded: chain R residue  305 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 53 optimal weight:    0.5980
   chunk 90 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 91 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
N  13 GLN
P   9 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.115587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.089029 restraints weight = 21142.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.091776 restraints weight = 12236.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.093720 restraints weight = 8691.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.095054 restraints weight = 6890.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.095825 restraints weight = 5864.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.3456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8938  Z= 0.116
  Angle     :  0.579  13.889  12115  Z= 0.296
  Chirality :  0.041   0.148   1360
  Planarity :  0.003   0.050   1550
  Dihedral  :  4.057  33.023   1229
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 18.38 %
    Favored  : 79.40 %
  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 (0.26), residues: 1103
  helix:  1.71 (0.25), residues: 435
  sheet:  0.34 (0.34), residues: 220
  loop : -0.39 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  20 
 TYR   0.018   0.001   TYR R 157 
 PHE   0.029   0.001   PHE R 260 
 TRP   0.008   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 8932)
  covalent geometry    : angle       0.57883 (12103)
  SS BOND              : bond        0.00280 (    6)
  SS BOND              : angle       0.35712 (   12)
  hydrogen bonds       : bond        0.03688 (  454)
  hydrogen bonds       : angle       4.34470 ( 1281)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 152
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  360 TYR cc_start: 0.8776 (m-80) cc_final: 0.8247 (m-80)
REVERT: A  391 TYR cc_start: 0.8257 (OUTLIER) cc_final: 0.7439 (t80)
REVERT: B   49 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7446 (mtt-85)
REVERT: B   93 ILE cc_start: 0.8141 (mm) cc_final: 0.7941 (mm)
REVERT: B  217 MET cc_start: 0.8262 (pmm) cc_final: 0.7981 (pmm)
REVERT: B  260 GLU cc_start: 0.8091 (tt0) cc_final: 0.7857 (tt0)
REVERT: G   32 LYS cc_start: 0.9086 (mmmm) cc_final: 0.8865 (mmmt)
REVERT: N   13 GLN cc_start: 0.6975 (OUTLIER) cc_final: 0.6655 (mm-40)
REVERT: N   47 TRP cc_start: 0.8170 (t60) cc_final: 0.7722 (t60)
REVERT: R   87 ASP cc_start: 0.8154 (m-30) cc_final: 0.7375 (t70)
REVERT: R  269 TYR cc_start: 0.8774 (m-10) cc_final: 0.8454 (m-80)
REVERT: R  305 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8318 (mm)
REVERT: R  378 LYS cc_start: 0.8622 (mtpp) cc_final: 0.8405 (mttm)
REVERT: P    9 ASN cc_start: 0.8627 (m-40) cc_final: 0.7869 (m-40)
REVERT: P   15 LYS cc_start: 0.9056 (ttmm) cc_final: 0.8671 (tmmt)
  outliers start: 20
  outliers final: 11
  residues processed: 163
  average time/residue: 0.1113
  time to fit residues: 24.4143
Evaluate side-chains
  157 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 142
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ASN
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   49 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  335 PHE
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   13 GLN
Chi-restraints excluded: chain N residue   60 TYR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  109 ASP
Chi-restraints excluded: chain R residue  271 ILE
Chi-restraints excluded: chain R residue  305 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 97 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 107 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 72 optimal weight:   30.0000
   chunk 99 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
N  13 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.115410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.088934 restraints weight = 21208.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.091707 restraints weight = 12301.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.093648 restraints weight = 8651.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.094917 restraints weight = 6830.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.095686 restraints weight = 5831.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.3558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8938  Z= 0.127
  Angle     :  0.590  11.368  12115  Z= 0.306
  Chirality :  0.041   0.172   1360
  Planarity :  0.003   0.050   1550
  Dihedral  :  3.995  31.551   1229
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.72 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 18.60 %
    Favored  : 79.18 %
  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:  0.84 (0.26), residues: 1103
  helix:  1.73 (0.25), residues: 435
  sheet:  0.49 (0.35), residues: 210
  loop : -0.52 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  20 
 TYR   0.017   0.001   TYR R 157 
 PHE   0.011   0.001   PHE R 178 
 TRP   0.008   0.001   TRP A 234 
 HIS   0.003   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 8932)
  covalent geometry    : angle       0.59043 (12103)
  SS BOND              : bond        0.00256 (    6)
  SS BOND              : angle       0.31326 (   12)
  hydrogen bonds       : bond        0.03677 (  454)
  hydrogen bonds       : angle       4.34260 ( 1281)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 149
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  360 TYR cc_start: 0.8797 (m-80) cc_final: 0.8212 (m-80)
REVERT: A  391 TYR cc_start: 0.8327 (OUTLIER) cc_final: 0.7556 (t80)
REVERT: B   49 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7465 (mtt-85)
REVERT: B   93 ILE cc_start: 0.8209 (mm) cc_final: 0.8003 (mm)
REVERT: B  217 MET cc_start: 0.8266 (pmm) cc_final: 0.7916 (pmm)
REVERT: B  260 GLU cc_start: 0.8133 (tt0) cc_final: 0.7897 (tt0)
REVERT: G   20 LYS cc_start: 0.9286 (mtmm) cc_final: 0.8855 (mtmm)
REVERT: N   13 GLN cc_start: 0.7009 (OUTLIER) cc_final: 0.6623 (mm-40)
REVERT: N   47 TRP cc_start: 0.8187 (t60) cc_final: 0.7732 (t60)
REVERT: R   87 ASP cc_start: 0.8193 (m-30) cc_final: 0.7398 (t70)
REVERT: R  269 TYR cc_start: 0.8745 (m-10) cc_final: 0.8411 (m-80)
REVERT: R  305 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8306 (mm)
REVERT: R  378 LYS cc_start: 0.8601 (mtpp) cc_final: 0.8386 (mttm)
REVERT: P    9 ASN cc_start: 0.8654 (m-40) cc_final: 0.7891 (m-40)
REVERT: P   15 LYS cc_start: 0.9047 (ttmm) cc_final: 0.8675 (tmmt)
  outliers start: 20
  outliers final: 14
  residues processed: 160
  average time/residue: 0.1142
  time to fit residues: 24.5888
Evaluate side-chains
  163 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 145
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ASN
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   49 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   13 GLN
Chi-restraints excluded: chain N residue   60 TYR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  109 ASP
Chi-restraints excluded: chain R residue  263 ARG
Chi-restraints excluded: chain R residue  271 ILE
Chi-restraints excluded: chain R residue  305 LEU
Chi-restraints excluded: chain P residue    2 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 95 optimal weight:    5.9990
   chunk 105 optimal weight:    0.8980
   chunk 82 optimal weight:    0.7980
   chunk 81 optimal weight:    7.9990
   chunk 56 optimal weight:    8.9990
   chunk 15 optimal weight:    2.9990
   chunk 64 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   chunk 76 optimal weight:   50.0000
   chunk 65 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.112325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.085793 restraints weight = 21169.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.088428 restraints weight = 12387.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.090290 restraints weight = 8807.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.091533 restraints weight = 7009.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.092169 restraints weight = 6023.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.3826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   8938  Z= 0.208
  Angle     :  0.653  13.431  12115  Z= 0.338
  Chirality :  0.043   0.178   1360
  Planarity :  0.004   0.052   1550
  Dihedral  :  4.270  35.732   1229
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.08 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 18.83 %
    Favored  : 78.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.26), residues: 1103
  helix:  1.66 (0.25), residues: 435
  sheet:  0.01 (0.33), residues: 233
  loop : -0.48 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 317 
 TYR   0.017   0.002   TYR R 157 
 PHE   0.021   0.002   PHE R 394 
 TRP   0.009   0.001   TRP A 234 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 8932)
  covalent geometry    : angle       0.65315 (12103)
  SS BOND              : bond        0.00316 (    6)
  SS BOND              : angle       0.36425 (   12)
  hydrogen bonds       : bond        0.04302 (  454)
  hydrogen bonds       : angle       4.55265 ( 1281)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  360 TYR cc_start: 0.8888 (m-80) cc_final: 0.8290 (m-80)
REVERT: A  391 TYR cc_start: 0.8401 (OUTLIER) cc_final: 0.7435 (t80)
REVERT: B   93 ILE cc_start: 0.8398 (mm) cc_final: 0.8037 (mm)
REVERT: G   42 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8519 (mm-30)
REVERT: N   47 TRP cc_start: 0.8284 (t60) cc_final: 0.7814 (t60)
REVERT: R   87 ASP cc_start: 0.8283 (m-30) cc_final: 0.7474 (t70)
REVERT: R  305 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8344 (mm)
REVERT: R  378 LYS cc_start: 0.8657 (mtpp) cc_final: 0.8418 (mttm)
REVERT: P    9 ASN cc_start: 0.8676 (m-40) cc_final: 0.7884 (m-40)
REVERT: P   15 LYS cc_start: 0.9064 (ttmm) cc_final: 0.8702 (tmmt)
  outliers start: 22
  outliers final: 19
  residues processed: 152
  average time/residue: 0.1170
  time to fit residues: 23.9329
Evaluate side-chains
  158 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 137
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ASN
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  335 PHE
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   13 GLN
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain N residue  109 ASP
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  263 ARG
Chi-restraints excluded: chain R residue  271 ILE
Chi-restraints excluded: chain R residue  305 LEU
Chi-restraints excluded: chain R residue  359 ILE
Chi-restraints excluded: chain P residue    2 SER
Chi-restraints excluded: chain P residue    5 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 8 optimal weight:    0.0980
   chunk 39 optimal weight:    0.8980
   chunk 84 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 90 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 76 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
N  13 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.115361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.088981 restraints weight = 20908.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.091778 restraints weight = 12123.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.093710 restraints weight = 8521.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.095037 restraints weight = 6745.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.095916 restraints weight = 5737.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.3807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8938  Z= 0.121
  Angle     :  0.609  11.907  12115  Z= 0.315
  Chirality :  0.041   0.147   1360
  Planarity :  0.003   0.049   1550
  Dihedral  :  4.002  34.789   1229
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.90 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 19.82 %
    Favored  : 78.29 %
  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:  0.78 (0.26), residues: 1103
  helix:  1.77 (0.25), residues: 436
  sheet:  0.25 (0.34), residues: 221
  loop : -0.56 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  20 
 TYR   0.017   0.001   TYR R 157 
 PHE   0.020   0.001   PHE R 394 
 TRP   0.008   0.001   TRP B 339 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 8932)
  covalent geometry    : angle       0.60954 (12103)
  SS BOND              : bond        0.00225 (    6)
  SS BOND              : angle       0.38995 (   12)
  hydrogen bonds       : bond        0.03680 (  454)
  hydrogen bonds       : angle       4.34175 ( 1281)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 148
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  360 TYR cc_start: 0.8780 (m-80) cc_final: 0.8195 (m-80)
REVERT: A  391 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7511 (t80)
REVERT: B   49 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7381 (mtt-85)
REVERT: B   93 ILE cc_start: 0.8346 (mm) cc_final: 0.7907 (mm)
REVERT: B  260 GLU cc_start: 0.8170 (tt0) cc_final: 0.7944 (tt0)
REVERT: G   29 LYS cc_start: 0.8898 (mmmt) cc_final: 0.8654 (mmmt)
REVERT: G   42 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8477 (mm-30)
REVERT: N   13 GLN cc_start: 0.7122 (OUTLIER) cc_final: 0.6774 (mm-40)
REVERT: N   47 TRP cc_start: 0.8196 (t60) cc_final: 0.7736 (t60)
REVERT: R   87 ASP cc_start: 0.8229 (m-30) cc_final: 0.7391 (t70)
REVERT: R  269 TYR cc_start: 0.8742 (m-10) cc_final: 0.8402 (m-80)
REVERT: R  378 LYS cc_start: 0.8641 (mtpp) cc_final: 0.8394 (mttm)
REVERT: P    9 ASN cc_start: 0.8689 (m-40) cc_final: 0.7872 (m-40)
REVERT: P   15 LYS cc_start: 0.9037 (ttmm) cc_final: 0.8677 (ttpt)
  outliers start: 17
  outliers final: 13
  residues processed: 156
  average time/residue: 0.1091
  time to fit residues: 23.0107
Evaluate side-chains
  159 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 143
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   49 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   13 GLN
Chi-restraints excluded: chain N residue   60 TYR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  109 ASP
Chi-restraints excluded: chain R residue  263 ARG
Chi-restraints excluded: chain R residue  271 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 62 optimal weight:   10.0000
   chunk 85 optimal weight:    0.1980
   chunk 60 optimal weight:   10.0000
   chunk 93 optimal weight:    5.9990
   chunk 9 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   chunk 43 optimal weight:    7.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B   6 GLN
B 340 ASN
N  13 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.115591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.089193 restraints weight = 21045.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.091962 restraints weight = 12205.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.093935 restraints weight = 8614.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.095125 restraints weight = 6794.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.096096 restraints weight = 5833.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.3855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8938  Z= 0.121
  Angle     :  0.605  11.014  12115  Z= 0.312
  Chirality :  0.041   0.166   1360
  Planarity :  0.003   0.049   1550
  Dihedral  :  3.926  33.021   1229
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.99 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 20.27 %
    Favored  : 77.85 %
  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 (0.26), residues: 1103
  helix:  1.77 (0.25), residues: 436
  sheet:  0.27 (0.34), residues: 221
  loop : -0.59 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  20 
 TYR   0.017   0.001   TYR R 157 
 PHE   0.019   0.001   PHE R 394 
 TRP   0.008   0.001   TRP A 234 
 HIS   0.006   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 8932)
  covalent geometry    : angle       0.60517 (12103)
  SS BOND              : bond        0.00230 (    6)
  SS BOND              : angle       0.33089 (   12)
  hydrogen bonds       : bond        0.03629 (  454)
  hydrogen bonds       : angle       4.29310 ( 1281)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 153
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 LYS cc_start: 0.9368 (ttmt) cc_final: 0.9035 (ttpp)
REVERT: A  360 TYR cc_start: 0.8771 (m-80) cc_final: 0.8192 (m-80)
REVERT: A  391 TYR cc_start: 0.8372 (OUTLIER) cc_final: 0.7549 (t80)
REVERT: B   49 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7389 (mtt-85)
REVERT: B   93 ILE cc_start: 0.8328 (mm) cc_final: 0.7878 (mm)
REVERT: B  260 GLU cc_start: 0.8180 (tt0) cc_final: 0.7961 (tt0)
REVERT: G   20 LYS cc_start: 0.9148 (mtmm) cc_final: 0.8868 (mtmm)
REVERT: G   29 LYS cc_start: 0.8901 (mmmt) cc_final: 0.8657 (mmmt)
REVERT: G   42 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8475 (mm-30)
REVERT: N   13 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6574 (mm-40)
REVERT: N   47 TRP cc_start: 0.8196 (t60) cc_final: 0.7749 (t60)
REVERT: R   87 ASP cc_start: 0.8261 (m-30) cc_final: 0.7427 (t70)
REVERT: R  269 TYR cc_start: 0.8752 (m-10) cc_final: 0.8404 (m-80)
REVERT: R  378 LYS cc_start: 0.8639 (mtpp) cc_final: 0.8412 (mttm)
REVERT: P    9 ASN cc_start: 0.8704 (m-40) cc_final: 0.7868 (m-40)
REVERT: P   15 LYS cc_start: 0.9027 (ttmm) cc_final: 0.8671 (ttpt)
  outliers start: 17
  outliers final: 12
  residues processed: 161
  average time/residue: 0.1154
  time to fit residues: 24.9184
Evaluate side-chains
  161 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 146
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   49 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   13 GLN
Chi-restraints excluded: chain N residue   60 TYR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  109 ASP
Chi-restraints excluded: chain R residue  263 ARG
Chi-restraints excluded: chain R residue  271 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 78 optimal weight:    0.0670
   chunk 10 optimal weight:    0.9990
   chunk 91 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 37 optimal weight:    6.9990
   chunk 57 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   overall best weight:    0.6718

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
N  13 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.116016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.089611 restraints weight = 20849.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.092376 restraints weight = 12154.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.094311 restraints weight = 8582.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.095488 restraints weight = 6808.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.096467 restraints weight = 5851.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.3919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8938  Z= 0.119
  Angle     :  0.611  13.914  12115  Z= 0.312
  Chirality :  0.040   0.152   1360
  Planarity :  0.003   0.049   1550
  Dihedral  :  3.881  29.941   1229
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.08 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 20.38 %
    Favored  : 77.85 %
  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 (0.26), residues: 1103
  helix:  1.76 (0.25), residues: 436
  sheet:  0.27 (0.34), residues: 221
  loop : -0.58 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  20 
 TYR   0.017   0.001   TYR R 157 
 PHE   0.019   0.001   PHE R 394 
 TRP   0.009   0.001   TRP R 243 
 HIS   0.003   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8932)
  covalent geometry    : angle       0.61083 (12103)
  SS BOND              : bond        0.00233 (    6)
  SS BOND              : angle       0.29998 (   12)
  hydrogen bonds       : bond        0.03538 (  454)
  hydrogen bonds       : angle       4.27318 ( 1281)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1708.69 seconds
wall clock time: 30 minutes 27.68 seconds (1827.68 seconds total)