Starting phenix.real_space_refine
on Wed Mar  4 03:50:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7w0m_32244/03_2026/7w0m_32244.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w0m_32244/03_2026/7w0m_32244.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.71
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7w0m_32244/03_2026/7w0m_32244.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w0m_32244/03_2026/7w0m_32244.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w0m_32244/03_2026/7w0m_32244.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w0m_32244/03_2026/7w0m_32244.cif"
  }
  resolution = 3.71
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2101 atoms to isotropic.
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      67      5.16       5
     C    5690      2.51       5
     N    1509      2.21       5
     O    1663      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8929
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1758
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1758
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
    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: "C"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 418
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
    Chain: "R"
      Number of atoms: 2321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 2321
          Classifications: {'peptide': 290}
          Link IDs: {'PTRANS': 11, 'TRANS': 278}
    Chain: "S"
      Number of atoms: 1794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1794
          Classifications: {'peptide': 233}
          Link IDs: {'PTRANS': 10, 'TRANS': 222}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 37
          Unusual residues: {'8EH': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.85, per 1000 atoms: 0.21
  Number of scatterers: 8929
  At special positions: 0
  Unit cell: (92.65, 119.85, 131.75, 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      67     16.00
     O    1663      8.00
     N    1509      7.00
     C    5690      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 102 " - pdb=" SG  CYS R 181 " 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: 0.58
  Conformation dependent library (CDL) restraints added in 337.0 milliseconds
  

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2118

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 15 sheets defined
      36.1% alpha, 17.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.695A  pdb=" N   LYS A  51 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   GLN A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   MET A  53 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 4.037A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 271 through 279
      removed outlier: 3.503A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 296 through 310
      removed outlier: 3.883A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.878A  pdb=" N   GLN B   9 " --> pdb=" O   ASP B   5 " (cutoff:3.500A)
      removed outlier: 5.090A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   ALA B  21 " --> pdb=" O   GLN B  17 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   ARG B  22 " --> pdb=" O   ILE B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.835A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 282
      No H-bonds generated for 'chain 'B' and resid 280 through 282'
    Processing helix  chain 'C' and resid 39 through 55
      removed outlier: 3.562A  pdb=" N   GLN C  49 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   ASN C  55 " --> pdb=" O   LYS C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 60 through 74
      removed outlier: 3.561A  pdb=" N   LEU C  68 " --> pdb=" O   ALA C  64 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 30 through 55
    Processing helix  chain 'R' and resid 64 through 81
      removed outlier: 4.494A  pdb=" N   THR R  81 " --> pdb=" O   THR R  77 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 81 through 91
      removed outlier: 4.020A  pdb=" N   TRP R  85 " --> pdb=" O   THR R  81 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   THR R  89 " --> pdb=" O   TRP R  85 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   TYR R  90 " --> pdb=" O   ALA R  86 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 99 through 132
      removed outlier: 3.979A  pdb=" N   LYS R 103 " --> pdb=" O   THR R  99 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 148 through 162
      removed outlier: 4.604A  pdb=" N   TRP R 154 " --> pdb=" O   THR R 150 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 162 through 167
      removed outlier: 3.963A  pdb=" N   VAL R 166 " --> pdb=" O   MET R 162 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 192 through 231
      removed outlier: 4.080A  pdb=" N   ALA R 196 " --> pdb=" O   SER R 192 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   THR R 207 " --> pdb=" O   VAL R 203 " (cutoff:3.500A)
      Proline residue:  R 213  - end of helix
    Processing helix  chain 'R' and resid 238 through 276
      removed outlier: 4.087A  pdb=" N   LYS R 242 " --> pdb=" O   GLU R 238 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   VAL R 254 " --> pdb=" O   ILE R 250 " (cutoff:3.500A)
      Proline residue:  R 263  - end of helix
      removed outlier: 4.014A  pdb=" N   LEU R 276 " --> pdb=" O   MET R 272 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 281 through 291
      removed outlier: 4.361A  pdb=" N   LEU R 285 " --> pdb=" O   CYS R 281 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   PHE R 286 " --> pdb=" O   ASP R 282 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 293 through 304
      removed outlier: 4.244A  pdb=" N   ILE R 297 " --> pdb=" O   TYR R 293 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   SER R 302 " --> pdb=" O   SER R 298 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 306 through 311
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 52 through 56
      removed outlier: 3.781A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35
      removed outlier: 6.164A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39
      removed outlier: 3.577A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.071A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.837A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.193A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ASP B  83 " --> pdb=" O   ASN B  88 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.039A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.149A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.017A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151
      removed outlier: 3.820A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   TRP B 169 " --> pdb=" O   ILE B 157 " (cutoff:3.500A)
      removed outlier: 7.086A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 5.000A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.910A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.539A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.163A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 5.424A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 4.944A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'R' and resid 168 through 171
      removed outlier: 3.736A  pdb=" N   GLN R 180 " --> pdb=" O   GLY R 171 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 5 through 7
      removed outlier: 3.818A  pdb=" N   SER S  21 " --> pdb=" O   SER S   7 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LEU S  81 " --> pdb=" O   LEU S  20 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   THR S  78 " --> pdb=" O   ASP S  73 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ASP S  73 " --> pdb=" O   THR S  78 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   SER S  71 " --> pdb=" O   PHE S  80 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   THR S  69 " --> pdb=" O   GLN S  82 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 49 through 51
      removed outlier: 3.842A  pdb=" N   ALA S  49 " --> pdb=" O   TRP S  36 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   TRP S  36 " --> pdb=" O   ALA S  49 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   VAL S  97 " --> pdb=" O   HIS S  35 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 147
    Processing sheet with id=AB5, first strand: chain 'S' and resid 156 through 160
    Processing sheet with id=AB6, first strand: chain 'S' and resid 186 through 187

    352 hydrogen bonds defined for protein.
    1014 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: 1.43

  Time building geometry restraints manager: 0.84 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2854
        1.35 -     1.47: 2370
        1.47 -     1.60: 3801
        1.60 -     1.72: 1
        1.72 -     1.85: 98
  Bond restraints: 9124
  Sorted by residual:
  bond pdb=" C30 8EH R 401 "
       pdb=" C31 8EH R 401 "
    ideal  model  delta    sigma   weight residual
    1.472  1.569 -0.097 2.00e-02 2.50e+03 2.33e+01
  bond pdb=" C30 8EH R 401 "
       pdb=" N29 8EH R 401 "
    ideal  model  delta    sigma   weight residual
    1.313  1.399 -0.086 2.00e-02 2.50e+03 1.84e+01
  bond pdb=" C10 8EH R 401 "
       pdb=" N11 8EH R 401 "
    ideal  model  delta    sigma   weight residual
    1.421  1.500 -0.079 2.00e-02 2.50e+03 1.55e+01
  bond pdb=" C12 8EH R 401 "
       pdb=" N28 8EH R 401 "
    ideal  model  delta    sigma   weight residual
    1.307  1.386 -0.079 2.00e-02 2.50e+03 1.54e+01
  bond pdb=" C30 8EH R 401 "
       pdb=" N11 8EH R 401 "
    ideal  model  delta    sigma   weight residual
    1.375  1.446 -0.071 2.00e-02 2.50e+03 1.27e+01
  ... (remaining 9119 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.46: 12147
        2.46 -     4.91: 180
        4.91 -     7.37: 31
        7.37 -     9.82: 6
        9.82 -    12.28: 1
  Bond angle restraints: 12365
  Sorted by residual:
  angle pdb=" C   LEU R 167 "
        pdb=" N   ARG R 168 "
        pdb=" CA  ARG R 168 "
      ideal   model   delta    sigma   weight residual
     120.75  128.01   -7.26 1.51e+00 4.39e-01 2.31e+01
  angle pdb=" CA  VAL R 166 "
        pdb=" CB  VAL R 166 "
        pdb=" CG2 VAL R 166 "
      ideal   model   delta    sigma   weight residual
     110.40  117.90   -7.50 1.70e+00 3.46e-01 1.94e+01
  angle pdb=" O15 8EH R 401 "
        pdb=" S14 8EH R 401 "
        pdb=" O16 8EH R 401 "
      ideal   model   delta    sigma   weight residual
     119.97  107.69   12.28 3.00e+00 1.11e-01 1.68e+01
  angle pdb=" N   VAL R 148 "
        pdb=" CA  VAL R 148 "
        pdb=" C   VAL R 148 "
      ideal   model   delta    sigma   weight residual
     112.96  108.95    4.01 1.00e+00 1.00e+00 1.61e+01
  angle pdb=" CA  GLU S 234 "
        pdb=" C   GLU S 234 "
        pdb=" O   GLU S 234 "
      ideal   model   delta    sigma   weight residual
     121.16  116.83    4.33 1.12e+00 7.97e-01 1.50e+01
  ... (remaining 12360 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 4863
       17.87 -    35.74: 444
       35.74 -    53.61: 62
       53.61 -    71.48: 15
       71.48 -    89.35: 12
  Dihedral angle restraints: 5396
    sinusoidal: 2108
      harmonic: 3288
  Sorted by residual:
  dihedral pdb=" CB  CYS R 102 "
           pdb=" SG  CYS R 102 "
           pdb=" SG  CYS R 181 "
           pdb=" CB  CYS R 181 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  171.61  -78.61     1      1.00e+01 1.00e-02 7.70e+01
  dihedral pdb=" CA  TYR S  94 "
           pdb=" C   TYR S  94 "
           pdb=" N   TYR S  95 "
           pdb=" CA  TYR S  95 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.31   25.69     0      5.00e+00 4.00e-02 2.64e+01
  dihedral pdb=" CA  THR B 164 "
           pdb=" C   THR B 164 "
           pdb=" N   THR B 165 "
           pdb=" CA  THR B 165 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.94  -21.06     0      5.00e+00 4.00e-02 1.77e+01
  ... (remaining 5393 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 1257
       0.072 -    0.144: 128
       0.144 -    0.217: 4
       0.217 -    0.289: 2
       0.289 -    0.361: 3
  Chirality restraints: 1394
  Sorted by residual:
  chirality pdb=" C19 8EH R 401 "
            pdb=" C17 8EH R 401 "
            pdb=" C21 8EH R 401 "
            pdb=" O20 8EH R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.43   -2.79    0.36 2.00e-01 2.50e+01 3.25e+00
  chirality pdb=" CA  LEU S 233 "
            pdb=" N   LEU S 233 "
            pdb=" C   LEU S 233 "
            pdb=" CB  LEU S 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.84   -0.33 2.00e-01 2.50e+01 2.79e+00
  chirality pdb=" CB  VAL R 166 "
            pdb=" CA  VAL R 166 "
            pdb=" CG1 VAL R 166 "
            pdb=" CG2 VAL R 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.32 2.00e-01 2.50e+01 2.53e+00
  ... (remaining 1391 not shown)

  Planarity restraints: 1555
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL S 147 "    0.040 5.00e-02 4.00e+02   6.06e-02 5.87e+00
        pdb=" N   PRO S 148 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO S 148 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO S 148 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP R 313 "   -0.040 5.00e-02 4.00e+02   5.93e-02 5.62e+00
        pdb=" N   PRO R 314 "    0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO R 314 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO R 314 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP R  95 "    0.032 5.00e-02 4.00e+02   4.93e-02 3.89e+00
        pdb=" N   PRO R  96 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO R  96 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO R  96 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1552 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1558
        2.76 -     3.30: 8547
        3.30 -     3.83: 13975
        3.83 -     4.37: 15727
        4.37 -     4.90: 27291
  Nonbonded interactions: 67098
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  97 "
            pdb=" OD2 ASP B 118 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" NE  ARG R  91 "
            pdb=" O   ASP R  94 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" OE1 GLN B 176 "
            pdb=" OG1 THR B 179 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" O   THR A 327 "
            pdb=" N   LYS A 330 "
     model   vdw
     2.272 3.120
  nonbonded pdb=" ND2 ASN R  46 "
            pdb=" O   ALA R  72 "
     model   vdw
     2.277 3.120
  ... (remaining 67093 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:             3.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.870
  Find NCS groups from input model:        0.050
  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:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7203
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      :  0.004   0.100   9125  Z= 0.224
  Angle     :  0.761  12.279  12367  Z= 0.405
  Chirality :  0.047   0.361   1394
  Planarity :  0.005   0.076   1555
  Dihedral  : 14.112  89.348   3275
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.90 (0.25), residues: 1118
  helix:  0.51 (0.29), residues: 352
  sheet: -1.72 (0.32), residues: 256
  loop : -2.30 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 315 
 TYR   0.022   0.002   TYR S 235 
 PHE   0.027   0.001   PHE S  27 
 TRP   0.026   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 9124)
  covalent geometry    : angle       0.76062 (12365)
  SS BOND              : bond        0.00013 (    1)
  SS BOND              : angle       1.33790 (    2)
  hydrogen bonds       : bond        0.16688 (  352)
  hydrogen bonds       : angle       5.91827 ( 1014)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 310
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7512 (tm-30)
REVERT: A  191 PHE cc_start: 0.8395 (t80) cc_final: 0.8183 (t80)
REVERT: A  193 ASP cc_start: 0.7955 (m-30) cc_final: 0.7741 (m-30)
REVERT: A  245 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7717 (mm-30)
REVERT: A  271 LYS cc_start: 0.8171 (tptp) cc_final: 0.7911 (tptt)
REVERT: A  344 ILE cc_start: 0.7883 (tt) cc_final: 0.7677 (tt)
REVERT: A  348 LEU cc_start: 0.7514 (tp) cc_final: 0.7254 (tt)
REVERT: B   25 CYS cc_start: 0.8399 (m) cc_final: 0.7911 (t)
REVERT: B   61 MET cc_start: 0.6892 (tmm) cc_final: 0.6578 (tmm)
REVERT: B  124 TYR cc_start: 0.8294 (m-80) cc_final: 0.7711 (m-80)
REVERT: B  197 ARG cc_start: 0.7869 (mtp85) cc_final: 0.7578 (mtp85)
REVERT: B  199 PHE cc_start: 0.8189 (p90) cc_final: 0.7933 (p90)
REVERT: B  212 ASP cc_start: 0.7593 (t0) cc_final: 0.7318 (t70)
REVERT: B  220 GLN cc_start: 0.7811 (mt0) cc_final: 0.7520 (mt0)
REVERT: B  233 CYS cc_start: 0.7497 (t) cc_final: 0.7115 (t)
REVERT: B  247 ASP cc_start: 0.7413 (t0) cc_final: 0.7060 (t0)
REVERT: B  314 ARG cc_start: 0.7502 (ptp-170) cc_final: 0.7216 (ptm160)
REVERT: R   97 PHE cc_start: 0.7240 (m-10) cc_final: 0.7018 (m-10)
REVERT: R  162 MET cc_start: 0.5535 (mmp) cc_final: 0.5175 (mmp)
REVERT: R  165 MET cc_start: 0.7280 (tpt) cc_final: 0.6920 (tpt)
REVERT: R  166 VAL cc_start: 0.7767 (t) cc_final: 0.7111 (t)
REVERT: R  183 MET cc_start: 0.4866 (tmm) cc_final: 0.4437 (tmm)
REVERT: R  268 LYS cc_start: 0.8837 (mttt) cc_final: 0.8499 (mttt)
REVERT: R  284 ASP cc_start: 0.8074 (t0) cc_final: 0.7810 (t0)
REVERT: R  301 ASN cc_start: 0.7790 (t0) cc_final: 0.7429 (t0)
REVERT: S   34 MET cc_start: 0.7776 (mmm) cc_final: 0.7165 (mmm)
REVERT: S   85 SER cc_start: 0.7950 (p) cc_final: 0.7679 (m)
REVERT: S   89 GLU cc_start: 0.7756 (tp30) cc_final: 0.7500 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 310
  average time/residue: 0.0972
  time to fit residues: 40.5937
Evaluate side-chains
  279 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 279
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0050
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    3.9990
   chunk 106 optimal weight:    2.9990
   overall best weight:    0.9796

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
B 175 GLN
B 259 GLN
R 112 ASN
** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  39 GLN
S 186 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.140564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.114917 restraints weight = 15408.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.118419 restraints weight = 8235.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.120755 restraints weight = 5295.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.122283 restraints weight = 3863.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.123321 restraints weight = 3100.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7225
moved from start:          0.1312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9125  Z= 0.188
  Angle     :  0.672   8.543  12367  Z= 0.347
  Chirality :  0.044   0.243   1394
  Planarity :  0.004   0.050   1555
  Dihedral  :  8.737  71.081   1261
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 13.30 %
    Favored  : 85.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.82 (0.24), residues: 1118
  helix:  0.57 (0.28), residues: 353
  sheet: -1.50 (0.32), residues: 252
  loop : -2.36 (0.24), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 205 
 TYR   0.031   0.002   TYR S 235 
 PHE   0.015   0.002   PHE B 199 
 TRP   0.017   0.002   TRP R 261 
 HIS   0.006   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 9124)
  covalent geometry    : angle       0.67213 (12365)
  SS BOND              : bond        0.00235 (    1)
  SS BOND              : angle       1.04833 (    2)
  hydrogen bonds       : bond        0.04739 (  352)
  hydrogen bonds       : angle       4.80077 ( 1014)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 279
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7633 (tm-30)
REVERT: A   26 ASP cc_start: 0.7897 (t0) cc_final: 0.7431 (t0)
REVERT: A  193 ASP cc_start: 0.7824 (m-30) cc_final: 0.7617 (m-30)
REVERT: A  205 ARG cc_start: 0.7214 (mmp80) cc_final: 0.6976 (mmp80)
REVERT: A  216 GLU cc_start: 0.7690 (tp30) cc_final: 0.7444 (tp30)
REVERT: A  245 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7536 (mm-30)
REVERT: A  248 LYS cc_start: 0.8739 (mttt) cc_final: 0.8507 (tttt)
REVERT: A  344 ILE cc_start: 0.8082 (tt) cc_final: 0.7862 (tt)
REVERT: A  348 LEU cc_start: 0.7809 (tp) cc_final: 0.7542 (tt)
REVERT: B   25 CYS cc_start: 0.8248 (m) cc_final: 0.7913 (t)
REVERT: B   59 TYR cc_start: 0.8415 (m-80) cc_final: 0.7898 (m-80)
REVERT: B   61 MET cc_start: 0.6903 (tmm) cc_final: 0.6431 (tmm)
REVERT: B  153 ASP cc_start: 0.7372 (p0) cc_final: 0.7170 (p0)
REVERT: B  197 ARG cc_start: 0.7774 (mtp85) cc_final: 0.7535 (mtp85)
REVERT: B  233 CYS cc_start: 0.7574 (t) cc_final: 0.7201 (t)
REVERT: B  291 ASP cc_start: 0.6733 (p0) cc_final: 0.6524 (p0)
REVERT: R  166 VAL cc_start: 0.7551 (OUTLIER) cc_final: 0.7006 (t)
REVERT: R  183 MET cc_start: 0.4880 (tmm) cc_final: 0.4251 (tmm)
REVERT: R  268 LYS cc_start: 0.8791 (mttt) cc_final: 0.8459 (mttt)
REVERT: R  284 ASP cc_start: 0.7947 (t0) cc_final: 0.7694 (t0)
REVERT: S   34 MET cc_start: 0.7706 (mmm) cc_final: 0.6940 (mmm)
REVERT: S  117 LEU cc_start: 0.8569 (mp) cc_final: 0.8333 (mt)
  outliers start: 14
  outliers final: 7
  residues processed: 283
  average time/residue: 0.0901
  time to fit residues: 35.4005
Evaluate side-chains
  282 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 274
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue  166 VAL
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 69 optimal weight:    8.9990
   chunk 23 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 99 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 16 optimal weight:    0.5980
   chunk 51 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 10 optimal weight:    0.3980
   chunk 108 optimal weight:    4.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
R 112 ASN
** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 169 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.141280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.115496 restraints weight = 15256.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.119028 restraints weight = 8013.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.121405 restraints weight = 5070.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.122737 restraints weight = 3657.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.123942 restraints weight = 2963.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.1627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9125  Z= 0.149
  Angle     :  0.620   8.074  12367  Z= 0.321
  Chirality :  0.043   0.251   1394
  Planarity :  0.004   0.042   1555
  Dihedral  :  8.556  69.370   1261
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.70 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.71 (0.24), residues: 1118
  helix:  0.59 (0.28), residues: 354
  sheet: -1.29 (0.32), residues: 252
  loop : -2.34 (0.24), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  52 
 TYR   0.029   0.002   TYR S 235 
 PHE   0.025   0.001   PHE S  27 
 TRP   0.013   0.001   TRP R 261 
 HIS   0.005   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 9124)
  covalent geometry    : angle       0.62027 (12365)
  SS BOND              : bond        0.00259 (    1)
  SS BOND              : angle       0.92124 (    2)
  hydrogen bonds       : bond        0.04256 (  352)
  hydrogen bonds       : angle       4.60008 ( 1014)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 273
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7591 (tm-30)
REVERT: A   26 ASP cc_start: 0.7881 (t0) cc_final: 0.7413 (t0)
REVERT: A  193 ASP cc_start: 0.7844 (m-30) cc_final: 0.7629 (m-30)
REVERT: A  216 GLU cc_start: 0.7700 (tp30) cc_final: 0.7448 (tp30)
REVERT: A  245 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7474 (mm-30)
REVERT: A  271 LYS cc_start: 0.8134 (tptp) cc_final: 0.7885 (tptt)
REVERT: A  330 LYS cc_start: 0.8191 (mmmm) cc_final: 0.7897 (mmmm)
REVERT: A  348 LEU cc_start: 0.7887 (tp) cc_final: 0.7604 (tt)
REVERT: B   25 CYS cc_start: 0.8172 (m) cc_final: 0.7924 (t)
REVERT: B   61 MET cc_start: 0.6894 (tmm) cc_final: 0.6395 (tmm)
REVERT: B  180 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.6795 (p90)
REVERT: B  188 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.7431 (mmt)
REVERT: B  191 SER cc_start: 0.8595 (t) cc_final: 0.8094 (t)
REVERT: B  233 CYS cc_start: 0.7556 (t) cc_final: 0.7229 (t)
REVERT: B  291 ASP cc_start: 0.6653 (p0) cc_final: 0.6437 (p0)
REVERT: B  317 CYS cc_start: 0.7589 (p) cc_final: 0.7216 (p)
REVERT: R   36 MET cc_start: 0.6339 (mmp) cc_final: 0.6130 (mmp)
REVERT: R   78 PHE cc_start: 0.6678 (t80) cc_final: 0.6462 (t80)
REVERT: R  183 MET cc_start: 0.4913 (tmm) cc_final: 0.4207 (tmm)
REVERT: R  268 LYS cc_start: 0.8819 (mttt) cc_final: 0.8468 (mttt)
REVERT: R  284 ASP cc_start: 0.7916 (t0) cc_final: 0.7681 (t0)
REVERT: S  117 LEU cc_start: 0.8536 (mp) cc_final: 0.8316 (mt)
REVERT: S  230 MET cc_start: 0.7918 (ttp) cc_final: 0.7497 (ttt)
  outliers start: 24
  outliers final: 13
  residues processed: 286
  average time/residue: 0.0871
  time to fit residues: 34.6781
Evaluate side-chains
  287 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 272
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   31 ILE
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain S residue   25 SER
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  192 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   chunk 93 optimal weight:    0.5980
   chunk 70 optimal weight:    0.0970
   chunk 37 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 80 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9990
   chunk 62 optimal weight:    8.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 169 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.141478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.115466 restraints weight = 15606.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.119036 restraints weight = 8156.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.121396 restraints weight = 5148.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.122989 restraints weight = 3723.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.123899 restraints weight = 2968.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          0.1809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9125  Z= 0.138
  Angle     :  0.606   7.893  12367  Z= 0.311
  Chirality :  0.042   0.264   1394
  Planarity :  0.004   0.036   1555
  Dihedral  :  8.555  69.205   1261
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 18.35 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.66 (0.24), residues: 1118
  helix:  0.65 (0.28), residues: 357
  sheet: -1.22 (0.31), residues: 262
  loop : -2.36 (0.25), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 197 
 TYR   0.025   0.001   TYR S 235 
 PHE   0.012   0.001   PHE B 241 
 TRP   0.012   0.001   TRP S  47 
 HIS   0.005   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 9124)
  covalent geometry    : angle       0.60581 (12365)
  SS BOND              : bond        0.00275 (    1)
  SS BOND              : angle       0.83671 (    2)
  hydrogen bonds       : bond        0.04020 (  352)
  hydrogen bonds       : angle       4.45871 ( 1014)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 283
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7511 (tm-30)
REVERT: A   26 ASP cc_start: 0.7883 (t0) cc_final: 0.7411 (t0)
REVERT: A  193 ASP cc_start: 0.7852 (m-30) cc_final: 0.7636 (m-30)
REVERT: A  216 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7457 (tp30)
REVERT: A  245 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7474 (mm-30)
REVERT: A  271 LYS cc_start: 0.8108 (tptp) cc_final: 0.7886 (tptt)
REVERT: A  330 LYS cc_start: 0.8180 (mmmm) cc_final: 0.7915 (mmmm)
REVERT: A  348 LEU cc_start: 0.7869 (tp) cc_final: 0.7596 (tt)
REVERT: B   25 CYS cc_start: 0.8126 (m) cc_final: 0.7912 (t)
REVERT: B   61 MET cc_start: 0.6909 (tmm) cc_final: 0.6445 (tmm)
REVERT: B   82 TRP cc_start: 0.8316 (m100) cc_final: 0.7938 (m100)
REVERT: B  180 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.6931 (p90)
REVERT: B  188 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.7395 (mmt)
REVERT: B  191 SER cc_start: 0.8582 (t) cc_final: 0.8073 (t)
REVERT: B  233 CYS cc_start: 0.7612 (t) cc_final: 0.7327 (t)
REVERT: R  183 MET cc_start: 0.4906 (tmm) cc_final: 0.4238 (tmm)
REVERT: R  284 ASP cc_start: 0.7899 (t0) cc_final: 0.7669 (t0)
REVERT: S   34 MET cc_start: 0.7661 (mmm) cc_final: 0.6942 (mmm)
REVERT: S   50 TYR cc_start: 0.8375 (t80) cc_final: 0.8130 (t80)
  outliers start: 32
  outliers final: 22
  residues processed: 298
  average time/residue: 0.0850
  time to fit residues: 35.3934
Evaluate side-chains
  305 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 280
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   31 ILE
Chi-restraints excluded: chain R residue  113 MET
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  175 TYR
Chi-restraints excluded: chain S residue  183 GLN
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  224 VAL
Chi-restraints excluded: chain S residue  238 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 77 optimal weight:    0.1980
   chunk 92 optimal weight:    0.7980
   chunk 32 optimal weight:    0.0870
   chunk 20 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 169 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.143061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.116741 restraints weight = 15500.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.120227 restraints weight = 8170.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.122650 restraints weight = 5232.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.124251 restraints weight = 3795.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.125227 restraints weight = 3017.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
moved from start:          0.1953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9125  Z= 0.130
  Angle     :  0.600   8.005  12367  Z= 0.309
  Chirality :  0.042   0.273   1394
  Planarity :  0.004   0.037   1555
  Dihedral  :  8.550  68.224   1261
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 20.10 %
    Favored  : 76.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.56 (0.24), residues: 1118
  helix:  0.67 (0.28), residues: 358
  sheet: -1.10 (0.31), residues: 262
  loop : -2.30 (0.25), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 197 
 TYR   0.022   0.001   TYR S 235 
 PHE   0.012   0.001   PHE S  27 
 TRP   0.011   0.001   TRP S  47 
 HIS   0.004   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 9124)
  covalent geometry    : angle       0.60025 (12365)
  SS BOND              : bond        0.00244 (    1)
  SS BOND              : angle       0.80764 (    2)
  hydrogen bonds       : bond        0.03907 (  352)
  hydrogen bonds       : angle       4.40764 ( 1014)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 275
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7501 (tm-30)
REVERT: A   26 ASP cc_start: 0.7873 (t0) cc_final: 0.7411 (t0)
REVERT: A  193 ASP cc_start: 0.7843 (m-30) cc_final: 0.7627 (m-30)
REVERT: A  216 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7442 (tp30)
REVERT: A  245 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7485 (mm-30)
REVERT: A  348 LEU cc_start: 0.7867 (tp) cc_final: 0.7595 (tt)
REVERT: B   61 MET cc_start: 0.6906 (tmm) cc_final: 0.6447 (tmm)
REVERT: B   82 TRP cc_start: 0.8314 (m100) cc_final: 0.8033 (m100)
REVERT: B  180 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.6888 (p90)
REVERT: B  188 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7420 (mmt)
REVERT: B  191 SER cc_start: 0.8582 (t) cc_final: 0.8081 (t)
REVERT: B  233 CYS cc_start: 0.7630 (t) cc_final: 0.7379 (t)
REVERT: R   36 MET cc_start: 0.6231 (mmp) cc_final: 0.6022 (mmp)
REVERT: R  162 MET cc_start: 0.5409 (mmp) cc_final: 0.5106 (mmp)
REVERT: R  183 MET cc_start: 0.4851 (tmm) cc_final: 0.4155 (tmm)
REVERT: R  268 LYS cc_start: 0.8828 (mttt) cc_final: 0.8489 (mttt)
REVERT: S   50 TYR cc_start: 0.8424 (t80) cc_final: 0.8209 (t80)
REVERT: S  230 MET cc_start: 0.7883 (ttp) cc_final: 0.7560 (ttt)
  outliers start: 33
  outliers final: 24
  residues processed: 289
  average time/residue: 0.0815
  time to fit residues: 33.0484
Evaluate side-chains
  302 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 275
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   31 ILE
Chi-restraints excluded: chain R residue  113 MET
Chi-restraints excluded: chain R residue  123 LEU
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain S residue   93 MET
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  175 TYR
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  224 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 82 optimal weight:    0.5980
   chunk 78 optimal weight:    3.9990
   chunk 108 optimal weight:    4.9990
   chunk 90 optimal weight:    2.9990
   chunk 93 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0060
   chunk 67 optimal weight:    0.6980
   chunk 56 optimal weight:    3.9990
   chunk 22 optimal weight:    7.9990
   chunk 88 optimal weight:    2.9990
   chunk 58 optimal weight:    0.2980
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
S 169 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.143517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.117237 restraints weight = 15413.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.120764 restraints weight = 8116.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.123151 restraints weight = 5168.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.124688 restraints weight = 3752.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.125740 restraints weight = 2999.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9125  Z= 0.123
  Angle     :  0.602   8.125  12367  Z= 0.309
  Chirality :  0.042   0.271   1394
  Planarity :  0.004   0.048   1555
  Dihedral  :  8.417  67.612   1261
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 20.93 %
    Favored  : 75.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.47 (0.25), residues: 1118
  helix:  0.78 (0.29), residues: 357
  sheet: -0.98 (0.32), residues: 262
  loop : -2.32 (0.24), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 197 
 TYR   0.019   0.001   TYR S 235 
 PHE   0.016   0.001   PHE R  97 
 TRP   0.019   0.001   TRP R 261 
 HIS   0.003   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 9124)
  covalent geometry    : angle       0.60175 (12365)
  SS BOND              : bond        0.00217 (    1)
  SS BOND              : angle       0.71733 (    2)
  hydrogen bonds       : bond        0.03784 (  352)
  hydrogen bonds       : angle       4.32877 ( 1014)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 270
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7505 (tm-30)
REVERT: A   26 ASP cc_start: 0.7857 (t0) cc_final: 0.7392 (t0)
REVERT: A  216 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7443 (tp30)
REVERT: A  245 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7459 (mm-30)
REVERT: A  309 ASP cc_start: 0.7689 (t0) cc_final: 0.7482 (t0)
REVERT: A  348 LEU cc_start: 0.7852 (tp) cc_final: 0.7586 (tt)
REVERT: B   61 MET cc_start: 0.6913 (tmm) cc_final: 0.6445 (tmm)
REVERT: B   82 TRP cc_start: 0.8306 (m100) cc_final: 0.8028 (m100)
REVERT: B  180 PHE cc_start: 0.7632 (OUTLIER) cc_final: 0.6845 (p90)
REVERT: B  188 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7424 (mmt)
REVERT: B  191 SER cc_start: 0.8551 (t) cc_final: 0.8038 (t)
REVERT: B  233 CYS cc_start: 0.7664 (t) cc_final: 0.7412 (t)
REVERT: B  247 ASP cc_start: 0.7350 (t0) cc_final: 0.7019 (t0)
REVERT: R   36 MET cc_start: 0.6411 (mmp) cc_final: 0.6191 (mmp)
REVERT: R  162 MET cc_start: 0.5357 (mmp) cc_final: 0.5060 (mmp)
REVERT: R  183 MET cc_start: 0.4858 (tmm) cc_final: 0.4160 (tmm)
REVERT: R  268 LYS cc_start: 0.8824 (mttt) cc_final: 0.8462 (mttt)
REVERT: S  230 MET cc_start: 0.7847 (ttp) cc_final: 0.7500 (ttt)
  outliers start: 32
  outliers final: 25
  residues processed: 283
  average time/residue: 0.0797
  time to fit residues: 31.6849
Evaluate side-chains
  295 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 267
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain R residue   31 ILE
Chi-restraints excluded: chain R residue  113 MET
Chi-restraints excluded: chain R residue  123 LEU
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain S residue   25 SER
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  175 TYR
Chi-restraints excluded: chain S residue  183 GLN
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  224 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 58 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 109 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   chunk 75 optimal weight:    0.4980
   chunk 33 optimal weight:    1.9990
   chunk 71 optimal weight:    5.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
B 295 ASN
S 169 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.142054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.115801 restraints weight = 15520.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.119287 restraints weight = 8186.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.121640 restraints weight = 5263.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.123085 restraints weight = 3830.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.124219 restraints weight = 3092.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7226
moved from start:          0.2225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9125  Z= 0.153
  Angle     :  0.626   8.265  12367  Z= 0.324
  Chirality :  0.043   0.276   1394
  Planarity :  0.004   0.046   1555
  Dihedral  :  8.392  61.189   1261
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 21.13 %
    Favored  : 74.85 %
  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: -1.49 (0.24), residues: 1118
  helix:  0.75 (0.29), residues: 357
  sheet: -0.84 (0.33), residues: 247
  loop : -2.39 (0.24), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 197 
 TYR   0.018   0.002   TYR S 235 
 PHE   0.014   0.001   PHE B 241 
 TRP   0.012   0.001   TRP S  47 
 HIS   0.005   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 9124)
  covalent geometry    : angle       0.62605 (12365)
  SS BOND              : bond        0.00125 (    1)
  SS BOND              : angle       0.87261 (    2)
  hydrogen bonds       : bond        0.04001 (  352)
  hydrogen bonds       : angle       4.38099 ( 1014)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 269
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7533 (tm-30)
REVERT: A   26 ASP cc_start: 0.7901 (t0) cc_final: 0.7394 (t0)
REVERT: A  193 ASP cc_start: 0.7868 (m-30) cc_final: 0.7611 (m-30)
REVERT: A  200 ASP cc_start: 0.8420 (t0) cc_final: 0.8164 (t0)
REVERT: A  216 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7449 (tp30)
REVERT: A  245 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7461 (mm-30)
REVERT: A  248 LYS cc_start: 0.8684 (mttt) cc_final: 0.8473 (tttt)
REVERT: A  306 GLN cc_start: 0.7433 (OUTLIER) cc_final: 0.7114 (tt0)
REVERT: A  309 ASP cc_start: 0.7730 (t0) cc_final: 0.7493 (t0)
REVERT: A  347 ASN cc_start: 0.7803 (m110) cc_final: 0.7546 (m-40)
REVERT: A  348 LEU cc_start: 0.7814 (tp) cc_final: 0.7577 (tt)
REVERT: B   61 MET cc_start: 0.6926 (tmm) cc_final: 0.6455 (tmm)
REVERT: B   82 TRP cc_start: 0.8298 (m100) cc_final: 0.7992 (m100)
REVERT: B  180 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.6864 (p90)
REVERT: B  188 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7443 (mmt)
REVERT: B  191 SER cc_start: 0.8603 (OUTLIER) cc_final: 0.8109 (t)
REVERT: B  233 CYS cc_start: 0.7682 (t) cc_final: 0.7447 (t)
REVERT: B  243 THR cc_start: 0.8030 (p) cc_final: 0.7820 (p)
REVERT: R   36 MET cc_start: 0.6528 (mmp) cc_final: 0.6325 (mmp)
REVERT: R  162 MET cc_start: 0.5549 (mmp) cc_final: 0.5235 (mmp)
REVERT: R  183 MET cc_start: 0.4912 (tmm) cc_final: 0.4660 (tmm)
REVERT: R  268 LYS cc_start: 0.8824 (mttt) cc_final: 0.8437 (mttt)
REVERT: S  230 MET cc_start: 0.7873 (ttp) cc_final: 0.7569 (ttt)
  outliers start: 39
  outliers final: 26
  residues processed: 285
  average time/residue: 0.0784
  time to fit residues: 31.6960
Evaluate side-chains
  295 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 264
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  306 GLN
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain R residue   31 ILE
Chi-restraints excluded: chain R residue  113 MET
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain S residue   93 MET
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  175 TYR
Chi-restraints excluded: chain S residue  183 GLN
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  224 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 75 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0370
   chunk 90 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.7458

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
A 306 GLN
S 169 ASN

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 = 0.141712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.115550 restraints weight = 15418.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.119013 restraints weight = 8187.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.121369 restraints weight = 5260.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.122858 restraints weight = 3846.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.123890 restraints weight = 3099.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9125  Z= 0.153
  Angle     :  0.644   8.372  12367  Z= 0.329
  Chirality :  0.043   0.277   1394
  Planarity :  0.004   0.047   1555
  Dihedral  :  8.388  60.404   1261
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 22.06 %
    Favored  : 74.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.47 (0.24), residues: 1118
  helix:  0.74 (0.28), residues: 357
  sheet: -0.81 (0.33), residues: 246
  loop : -2.37 (0.24), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 197 
 TYR   0.019   0.002   TYR S 235 
 PHE   0.013   0.001   PHE B 241 
 TRP   0.011   0.001   TRP S  47 
 HIS   0.004   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 9124)
  covalent geometry    : angle       0.64373 (12365)
  SS BOND              : bond        0.00626 (    1)
  SS BOND              : angle       0.75961 (    2)
  hydrogen bonds       : bond        0.03999 (  352)
  hydrogen bonds       : angle       4.37309 ( 1014)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 269
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7524 (tm-30)
REVERT: A   26 ASP cc_start: 0.7883 (t0) cc_final: 0.7387 (t0)
REVERT: A  193 ASP cc_start: 0.7876 (m-30) cc_final: 0.7620 (m-30)
REVERT: A  197 LYS cc_start: 0.8103 (tttp) cc_final: 0.7577 (ttmm)
REVERT: A  200 ASP cc_start: 0.8445 (t0) cc_final: 0.8186 (t0)
REVERT: A  216 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7441 (tp30)
REVERT: A  245 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7476 (mm-30)
REVERT: A  307 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.7679 (t80)
REVERT: A  347 ASN cc_start: 0.7805 (m110) cc_final: 0.7529 (m-40)
REVERT: A  348 LEU cc_start: 0.7822 (tp) cc_final: 0.7584 (tt)
REVERT: B   61 MET cc_start: 0.6951 (tmm) cc_final: 0.6482 (tmm)
REVERT: B   82 TRP cc_start: 0.8294 (m100) cc_final: 0.7988 (m100)
REVERT: B  180 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.6783 (p90)
REVERT: B  188 MET cc_start: 0.7739 (mmt) cc_final: 0.7451 (mmt)
REVERT: B  191 SER cc_start: 0.8600 (OUTLIER) cc_final: 0.8102 (t)
REVERT: B  233 CYS cc_start: 0.7688 (t) cc_final: 0.7449 (t)
REVERT: B  243 THR cc_start: 0.8053 (p) cc_final: 0.7834 (p)
REVERT: B  247 ASP cc_start: 0.7486 (t0) cc_final: 0.7129 (t0)
REVERT: C   48 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7568 (mp0)
REVERT: R   36 MET cc_start: 0.6612 (mmp) cc_final: 0.6391 (mmp)
REVERT: R  162 MET cc_start: 0.5627 (mmp) cc_final: 0.5249 (mmp)
REVERT: R  169 THR cc_start: 0.7768 (t) cc_final: 0.7433 (t)
REVERT: R  183 MET cc_start: 0.4510 (tmm) cc_final: 0.3840 (tmm)
REVERT: R  268 LYS cc_start: 0.8815 (mttt) cc_final: 0.8421 (mttt)
REVERT: S   34 MET cc_start: 0.7692 (mmm) cc_final: 0.6952 (mmm)
REVERT: S  230 MET cc_start: 0.7892 (ttp) cc_final: 0.7591 (ttt)
  outliers start: 36
  outliers final: 25
  residues processed: 285
  average time/residue: 0.0840
  time to fit residues: 33.3553
Evaluate side-chains
  293 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 263
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   48 GLU
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain R residue   31 ILE
Chi-restraints excluded: chain R residue  113 MET
Chi-restraints excluded: chain R residue  262 MET
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  175 TYR
Chi-restraints excluded: chain S residue  183 GLN
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  224 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 101 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0030
   chunk 100 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 23 optimal weight:    4.9990
   chunk 82 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.6590

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
S 169 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.141296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.115277 restraints weight = 15303.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.118778 restraints weight = 8163.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.121122 restraints weight = 5220.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.122695 restraints weight = 3798.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.123613 restraints weight = 3030.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          0.2366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9125  Z= 0.146
  Angle     :  0.655   9.906  12367  Z= 0.334
  Chirality :  0.043   0.274   1394
  Planarity :  0.004   0.046   1555
  Dihedral  :  8.359  60.370   1261
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 22.27 %
    Favored  : 74.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.24), residues: 1118
  helix:  0.74 (0.28), residues: 357
  sheet: -0.87 (0.32), residues: 254
  loop : -2.31 (0.24), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 197 
 TYR   0.019   0.002   TYR S 235 
 PHE   0.012   0.001   PHE B 241 
 TRP   0.010   0.001   TRP S  47 
 HIS   0.004   0.001   HIS R 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 9124)
  covalent geometry    : angle       0.65511 (12365)
  SS BOND              : bond        0.00933 (    1)
  SS BOND              : angle       0.56100 (    2)
  hydrogen bonds       : bond        0.03909 (  352)
  hydrogen bonds       : angle       4.37629 ( 1014)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 266
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7537 (tm-30)
REVERT: A  193 ASP cc_start: 0.7880 (m-30) cc_final: 0.7624 (m-30)
REVERT: A  197 LYS cc_start: 0.8111 (tttp) cc_final: 0.7698 (ttmm)
REVERT: A  200 ASP cc_start: 0.8440 (t0) cc_final: 0.8182 (t0)
REVERT: A  216 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7493 (tp30)
REVERT: A  243 MET cc_start: 0.7274 (mtp) cc_final: 0.7072 (mtp)
REVERT: A  245 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7476 (mm-30)
REVERT: A  307 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.7655 (t80)
REVERT: A  309 ASP cc_start: 0.7755 (t0) cc_final: 0.7499 (t0)
REVERT: A  347 ASN cc_start: 0.7796 (m110) cc_final: 0.7538 (m-40)
REVERT: A  348 LEU cc_start: 0.7813 (tp) cc_final: 0.7576 (tt)
REVERT: B   61 MET cc_start: 0.6969 (tmm) cc_final: 0.6492 (tmm)
REVERT: B   82 TRP cc_start: 0.8288 (m100) cc_final: 0.7982 (m100)
REVERT: B  180 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.6760 (p90)
REVERT: B  188 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7422 (mmt)
REVERT: B  191 SER cc_start: 0.8570 (OUTLIER) cc_final: 0.8067 (t)
REVERT: B  233 CYS cc_start: 0.7704 (t) cc_final: 0.7470 (t)
REVERT: B  243 THR cc_start: 0.8061 (p) cc_final: 0.7832 (p)
REVERT: B  247 ASP cc_start: 0.7521 (t0) cc_final: 0.7141 (t0)
REVERT: C   48 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7576 (mp0)
REVERT: R  183 MET cc_start: 0.4642 (tmm) cc_final: 0.4103 (tmm)
REVERT: R  268 LYS cc_start: 0.8799 (mttt) cc_final: 0.8435 (mttt)
REVERT: S   34 MET cc_start: 0.7690 (mmm) cc_final: 0.6956 (mmm)
REVERT: S  230 MET cc_start: 0.7880 (ttp) cc_final: 0.7569 (ttt)
  outliers start: 35
  outliers final: 26
  residues processed: 280
  average time/residue: 0.0876
  time to fit residues: 33.9913
Evaluate side-chains
  297 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 265
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   48 GLU
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain R residue   31 ILE
Chi-restraints excluded: chain R residue  113 MET
Chi-restraints excluded: chain R residue  123 LEU
Chi-restraints excluded: chain R residue  216 ILE
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain S residue   93 MET
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  175 TYR
Chi-restraints excluded: chain S residue  183 GLN
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  224 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 50 optimal weight:    0.4980
   chunk 8 optimal weight:    0.0170
   chunk 39 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 88 optimal weight:    5.9990
   chunk 76 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 84 optimal weight:    3.9990
   overall best weight:    0.6418

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
S 169 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.142548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.116347 restraints weight = 15414.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.119844 restraints weight = 8234.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.122171 restraints weight = 5292.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.123688 restraints weight = 3868.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.124771 restraints weight = 3115.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9125  Z= 0.147
  Angle     :  0.681  11.617  12367  Z= 0.344
  Chirality :  0.044   0.279   1394
  Planarity :  0.005   0.091   1555
  Dihedral  :  8.370  60.752   1261
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 22.58 %
    Favored  : 73.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.46 (0.24), residues: 1118
  helix:  0.70 (0.28), residues: 357
  sheet: -0.83 (0.33), residues: 251
  loop : -2.31 (0.24), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 197 
 TYR   0.019   0.001   TYR S 235 
 PHE   0.012   0.001   PHE B 241 
 TRP   0.010   0.001   TRP S  36 
 HIS   0.004   0.001   HIS R 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 9124)
  covalent geometry    : angle       0.68110 (12365)
  SS BOND              : bond        0.01288 (    1)
  SS BOND              : angle       0.41424 (    2)
  hydrogen bonds       : bond        0.03921 (  352)
  hydrogen bonds       : angle       4.41045 ( 1014)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 266
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7513 (tm-30)
REVERT: A   26 ASP cc_start: 0.7860 (t0) cc_final: 0.7371 (t0)
REVERT: A  193 ASP cc_start: 0.7883 (m-30) cc_final: 0.7626 (m-30)
REVERT: A  197 LYS cc_start: 0.8116 (tttp) cc_final: 0.7699 (ttmm)
REVERT: A  200 ASP cc_start: 0.8437 (t0) cc_final: 0.8188 (t0)
REVERT: A  216 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7457 (tp30)
REVERT: A  245 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7468 (mm-30)
REVERT: A  307 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.7609 (t80)
REVERT: A  347 ASN cc_start: 0.7808 (m110) cc_final: 0.7524 (m-40)
REVERT: A  348 LEU cc_start: 0.7830 (tp) cc_final: 0.7592 (tt)
REVERT: B   61 MET cc_start: 0.6979 (tmm) cc_final: 0.6504 (tmm)
REVERT: B   82 TRP cc_start: 0.8291 (m100) cc_final: 0.7986 (m100)
REVERT: B  180 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.6767 (p90)
REVERT: B  191 SER cc_start: 0.8583 (OUTLIER) cc_final: 0.8082 (t)
REVERT: B  233 CYS cc_start: 0.7695 (t) cc_final: 0.7463 (t)
REVERT: B  243 THR cc_start: 0.8062 (p) cc_final: 0.7840 (p)
REVERT: C   48 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7608 (mp0)
REVERT: R  169 THR cc_start: 0.7652 (t) cc_final: 0.7373 (p)
REVERT: R  183 MET cc_start: 0.4557 (tmm) cc_final: 0.3870 (tmm)
REVERT: R  264 TYR cc_start: 0.7310 (t80) cc_final: 0.6080 (t80)
REVERT: R  268 LYS cc_start: 0.8806 (mttt) cc_final: 0.8302 (mttt)
REVERT: S   11 LEU cc_start: 0.8040 (mp) cc_final: 0.7770 (mm)
REVERT: S   34 MET cc_start: 0.7690 (mmm) cc_final: 0.6944 (mmm)
REVERT: S  230 MET cc_start: 0.7873 (ttp) cc_final: 0.7567 (ttt)
  outliers start: 35
  outliers final: 26
  residues processed: 281
  average time/residue: 0.0814
  time to fit residues: 32.1244
Evaluate side-chains
  297 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 266
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   48 GLU
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain R residue   31 ILE
Chi-restraints excluded: chain R residue  113 MET
Chi-restraints excluded: chain R residue  216 ILE
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain S residue   93 MET
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  175 TYR
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  224 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 108 optimal weight:    0.9980
   chunk 109 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
S 169 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.139463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.113607 restraints weight = 15211.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.117086 restraints weight = 8150.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.119441 restraints weight = 5215.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.120828 restraints weight = 3788.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.121937 restraints weight = 3076.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7244
moved from start:          0.2511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9125  Z= 0.186
  Angle     :  0.705  11.567  12367  Z= 0.358
  Chirality :  0.045   0.283   1394
  Planarity :  0.004   0.046   1555
  Dihedral  :  8.563  64.563   1261
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 22.58 %
    Favored  : 73.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.24), residues: 1118
  helix:  0.65 (0.28), residues: 358
  sheet: -0.86 (0.33), residues: 247
  loop : -2.33 (0.24), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R 168 
 TYR   0.020   0.002   TYR S 235 
 PHE   0.015   0.001   PHE B 241 
 TRP   0.012   0.001   TRP S  36 
 HIS   0.005   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 9124)
  covalent geometry    : angle       0.70470 (12365)
  SS BOND              : bond        0.00689 (    1)
  SS BOND              : angle       0.97673 (    2)
  hydrogen bonds       : bond        0.04251 (  352)
  hydrogen bonds       : angle       4.44524 ( 1014)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1602.28 seconds
wall clock time: 28 minutes 21.47 seconds (1701.47 seconds total)