Starting phenix.real_space_refine
on Wed Mar  4 04:10:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7w0p_32247/03_2026/7w0p_32247.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w0p_32247/03_2026/7w0p_32247.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7w0p_32247/03_2026/7w0p_32247.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w0p_32247/03_2026/7w0p_32247.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w0p_32247/03_2026/7w0p_32247.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w0p_32247/03_2026/7w0p_32247.cif"
  }
  resolution = 3.16
  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=   0.022
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 2057 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      68      5.16       5
     C    5788      2.51       5
     N    1541      2.21       5
     O    1694      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 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: 9091
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1813
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1813
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 2, 'TRANS': 222}
          Chain breaks: 1
    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: 2337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 2337
          Classifications: {'peptide': 292}
          Link IDs: {'PTRANS': 11, 'TRANS': 280}
    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: "D"
      Number of atoms: 128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 128
          Classifications: {'peptide': 15}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 11}
  Time building chain proxies: 2.15, per 1000 atoms: 0.24
  Number of scatterers: 9091
  At special positions: 0
  Unit cell: (90.48, 118.56, 132.08, 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      68     16.00
     O    1694      8.00
     N    1541      7.00
     C    5788      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: 0.64
  Conformation dependent library (CDL) restraints added in 281.1 milliseconds
  

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2166

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 13 sheets defined
      37.9% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 45 through 55
      removed outlier: 3.553A  pdb=" N   ILE A  55 " --> pdb=" O   LYS A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.714A  pdb=" N   LYS A 210 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TRP A 211 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.535A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   CYS A 214 " --> pdb=" O   TRP A 211 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   PHE A 215 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 207 through 216'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 4.049A  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 295 through 310
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 35
    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: 3.597A  pdb=" N   ASN C  55 " --> pdb=" O   LYS C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 60 through 76
    Processing helix  chain 'R' and resid 29 through 55
      removed outlier: 4.245A  pdb=" N   ALA R  33 " --> pdb=" O   ALA R  29 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   THR R  52 " --> pdb=" O   LEU R  48 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 64 through 80
    Processing helix  chain 'R' and resid 81 through 86
      removed outlier: 3.648A  pdb=" N   TRP R  85 " --> pdb=" O   THR R  81 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 87 through 92
    Processing helix  chain 'R' and resid 98 through 133
      removed outlier: 3.736A  pdb=" N   CYS R 102 " --> pdb=" O   GLY R  98 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   TYR R 107 " --> pdb=" O   LYS R 103 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   ARG R 133 " --> pdb=" O   LEU R 129 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 147
      removed outlier: 3.936A  pdb=" N   GLY R 146 " --> pdb=" O   LEU R 142 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   ALA R 147 " --> pdb=" O   ARG R 143 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 147 through 162
    Processing helix  chain 'R' and resid 163 through 165
      No H-bonds generated for 'chain 'R' and resid 163 through 165'
    Processing helix  chain 'R' and resid 190 through 233
      removed outlier: 4.159A  pdb=" N   TRP R 195 " --> pdb=" O   VAL R 191 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   GLY R 209 " --> pdb=" O   SER R 205 " (cutoff:3.500A)
      Proline residue:  R 213  - end of helix
      removed outlier: 4.276A  pdb=" N   ARG R 233 " --> pdb=" O   ALA R 229 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 236 through 274
      removed outlier: 4.230A  pdb=" N   ARG R 241 " --> pdb=" O   ILE R 237 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   LYS R 242 " --> pdb=" O   GLU R 238 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL R 254 " --> pdb=" O   ILE R 250 " (cutoff:3.500A)
      Proline residue:  R 263  - end of helix
    Processing helix  chain 'R' and resid 280 through 310
      removed outlier: 3.561A  pdb=" N   ASP R 284 " --> pdb=" O   PRO R 280 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   PHE R 286 " --> pdb=" O   ASP R 282 " (cutoff:3.500A)
      Proline residue:  R 292  - end of helix
      removed outlier: 3.893A  pdb=" N   CYS R 296 " --> pdb=" O   PRO R 292 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   ASN R 301 " --> pdb=" O   ILE R 297 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   SER R 302 " --> pdb=" O   SER R 298 " (cutoff:3.500A)
      Proline residue:  R 306  - end of helix
    Processing helix  chain 'R' and resid 313 through 317
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 74 through 76
      No H-bonds generated for 'chain 'S' and resid 74 through 76'
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.557A  pdb=" N   ASP S  90 " --> pdb=" O   ARG S  87 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 87 through 91'
    Processing helix  chain 'D' and resid 21 through 27
      removed outlier: 4.368A  pdb=" N   HIS D  26 " --> pdb=" O   CYS D  21 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.148A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.524A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.810A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.194A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52
      removed outlier: 5.535A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.773A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.954A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 5.919A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151
      removed outlier: 3.866A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.620A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.460A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.221A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.610A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.843A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 5 through 7
      removed outlier: 3.536A  pdb=" N   SER S  23 " --> pdb=" O   VAL S   5 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   THR S  78 " --> pdb=" O   ASP S  73 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ASP S  73 " --> pdb=" O   THR S  78 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 49 through 51
      removed outlier: 3.703A  pdb=" N   ALA S  49 " --> pdb=" O   TRP S  36 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 49 through 51
      removed outlier: 3.703A  pdb=" N   ALA S  49 " --> pdb=" O   TRP S  36 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 155 through 160
    Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195
      removed outlier: 3.852A  pdb=" N   ASN S 194 " --> pdb=" O   ARG S 191 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ARG S 191 " --> pdb=" O   ASN S 194 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LEU S 178 " --> pdb=" O   GLN S 186 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   TYR S 190 " --> pdb=" O   LEU S 174 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   LEU S 174 " --> pdb=" O   TYR S 190 " (cutoff:3.500A)

    409 hydrogen bonds defined for protein.
    1161 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: 1.16

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2910
        1.34 -     1.46: 1722
        1.46 -     1.58: 4556
        1.58 -     1.69: 0
        1.69 -     1.81: 100
  Bond restraints: 9288
  Sorted by residual:
  bond pdb=" C   ILE R  31 "
       pdb=" N   PRO R  32 "
    ideal  model  delta    sigma   weight residual
    1.335  1.369 -0.034 1.30e-02 5.92e+03 6.91e+00
  bond pdb=" N   VAL S   2 "
       pdb=" CA  VAL S   2 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.29e-02 6.01e+03 6.84e+00
  bond pdb=" N   ASP S   1 "
       pdb=" CA  ASP S   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.90e-02 2.77e+03 2.56e+00
  bond pdb=" CG1 ILE R 250 "
       pdb=" CD1 ILE R 250 "
    ideal  model  delta    sigma   weight residual
    1.513  1.452  0.061 3.90e-02 6.57e+02 2.46e+00
  bond pdb=" CB  CYS C  72 "
       pdb=" SG  CYS C  72 "
    ideal  model  delta    sigma   weight residual
    1.808  1.758  0.050 3.30e-02 9.18e+02 2.28e+00
  ... (remaining 9283 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 12307
        1.88 -     3.77: 221
        3.77 -     5.65: 42
        5.65 -     7.54: 10
        7.54 -     9.42: 4
  Bond angle restraints: 12584
  Sorted by residual:
  angle pdb=" C   ILE R  34 "
        pdb=" N   TYR R  35 "
        pdb=" CA  TYR R  35 "
      ideal   model   delta    sigma   weight residual
     121.14  113.90    7.24 1.75e+00 3.27e-01 1.71e+01
  angle pdb=" N   ILE B 270 "
        pdb=" CA  ILE B 270 "
        pdb=" C   ILE B 270 "
      ideal   model   delta    sigma   weight residual
     113.20  109.44    3.76 9.60e-01 1.09e+00 1.53e+01
  angle pdb=" C   ASP B 118 "
        pdb=" N   ASN B 119 "
        pdb=" CA  ASN B 119 "
      ideal   model   delta    sigma   weight residual
     121.54  128.43   -6.89 1.91e+00 2.74e-01 1.30e+01
  angle pdb=" C   MET R 113 "
        pdb=" N   TYR R 114 "
        pdb=" CA  TYR R 114 "
      ideal   model   delta    sigma   weight residual
     120.68  114.97    5.71 1.70e+00 3.46e-01 1.13e+01
  angle pdb=" CA  MET R 187 "
        pdb=" CB  MET R 187 "
        pdb=" CG  MET R 187 "
      ideal   model   delta    sigma   weight residual
     114.10  120.63   -6.53 2.00e+00 2.50e-01 1.07e+01
  ... (remaining 12579 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.46: 4949
       15.46 -    30.92: 437
       30.92 -    46.38: 99
       46.38 -    61.84: 13
       61.84 -    77.30: 2
  Dihedral angle restraints: 5500
    sinusoidal: 2140
      harmonic: 3360
  Sorted by residual:
  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 -155.30  -24.70     0      5.00e+00 4.00e-02 2.44e+01
  dihedral pdb=" CA  VAL D  29 "
           pdb=" C   VAL D  29 "
           pdb=" N   PRO D  30 "
           pdb=" CA  PRO D  30 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.08  -21.92     0      5.00e+00 4.00e-02 1.92e+01
  dihedral pdb=" CA  TYR S 190 "
           pdb=" C   TYR S 190 "
           pdb=" N   ARG S 191 "
           pdb=" CA  ARG S 191 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.44   20.56     0      5.00e+00 4.00e-02 1.69e+01
  ... (remaining 5497 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1054
       0.044 -    0.088: 276
       0.088 -    0.132: 78
       0.132 -    0.176: 9
       0.176 -    0.220: 4
  Chirality restraints: 1421
  Sorted by residual:
  chirality pdb=" CA  ASN R 305 "
            pdb=" N   ASN R 305 "
            pdb=" C   ASN R 305 "
            pdb=" CB  ASN R 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  VAL S   2 "
            pdb=" N   VAL S   2 "
            pdb=" C   VAL S   2 "
            pdb=" CB  VAL S   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CB  ILE S  58 "
            pdb=" CA  ILE S  58 "
            pdb=" CG1 ILE S  58 "
            pdb=" CG2 ILE S  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.86   -0.21 2.00e-01 2.50e+01 1.11e+00
  ... (remaining 1418 not shown)

  Planarity restraints: 1590
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR S 235 "   -0.042 5.00e-02 4.00e+02   6.31e-02 6.37e+00
        pdb=" N   PRO S 236 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO S 236 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO S 236 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR S 150 "   -0.039 5.00e-02 4.00e+02   5.93e-02 5.62e+00
        pdb=" N   PRO S 151 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO S 151 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO S 151 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.032 5.00e-02 4.00e+02   4.83e-02 3.73e+00
        pdb=" N   PRO B 236 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 1587 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 757
        2.74 -     3.28: 9303
        3.28 -     3.82: 15004
        3.82 -     4.36: 17273
        4.36 -     4.90: 30123
  Nonbonded interactions: 72460
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 290 "
            pdb=" O   SER A 293 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OH  TYR B 264 "
            pdb=" O   ALA B 299 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" OH  TYR R 114 "
            pdb=" O   ALA R 157 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OG  SER B 122 "
            pdb=" OE2 GLU B 138 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" ND2 ASN B 237 "
            pdb=" OD1 ASN B 239 "
     model   vdw
     2.280 3.120
  ... (remaining 72455 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.090
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6446
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   9289  Z= 0.153
  Angle     :  0.652   9.424  12586  Z= 0.350
  Chirality :  0.044   0.220   1421
  Planarity :  0.004   0.063   1590
  Dihedral  : 12.424  77.301   3331
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.57 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.97 (0.24), residues: 1142
  helix:  0.85 (0.27), residues: 372
  sheet: -0.08 (0.31), residues: 275
  loop : -2.21 (0.26), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 283 
 TYR   0.013   0.001   TYR R 107 
 PHE   0.014   0.001   PHE B 151 
 TRP   0.013   0.001   TRP R 195 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 9288)
  covalent geometry    : angle       0.65238 (12584)
  SS BOND              : bond        0.00241 (    1)
  SS BOND              : angle       0.26399 (    2)
  hydrogen bonds       : bond        0.16578 (  406)
  hydrogen bonds       : angle       6.75799 ( 1161)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 271
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.7772 (mptt) cc_final: 0.7254 (mptt)
REVERT: A   36 LEU cc_start: 0.7700 (mt) cc_final: 0.7466 (mp)
REVERT: A  194 LEU cc_start: 0.7963 (tp) cc_final: 0.7681 (tp)
REVERT: A  262 THR cc_start: 0.8384 (m) cc_final: 0.7787 (m)
REVERT: A  270 LYS cc_start: 0.7983 (mppt) cc_final: 0.7519 (mppt)
REVERT: A  275 GLU cc_start: 0.7324 (mt-10) cc_final: 0.7095 (mt-10)
REVERT: A  317 LYS cc_start: 0.7103 (ptmt) cc_final: 0.6852 (ptmt)
REVERT: A  321 THR cc_start: 0.8149 (t) cc_final: 0.7907 (t)
REVERT: A  333 GLN cc_start: 0.7648 (tp40) cc_final: 0.7073 (tp40)
REVERT: A  348 LEU cc_start: 0.8315 (mm) cc_final: 0.8095 (mm)
REVERT: A  349 LYS cc_start: 0.8057 (mttm) cc_final: 0.7715 (mttm)
REVERT: B   22 ARG cc_start: 0.6723 (ptp-110) cc_final: 0.6485 (ptp-110)
REVERT: B   61 MET cc_start: 0.7313 (ppp) cc_final: 0.6766 (ppp)
REVERT: B  120 ILE cc_start: 0.8236 (pt) cc_final: 0.8033 (pt)
REVERT: B  155 ASN cc_start: 0.7044 (t0) cc_final: 0.6668 (t0)
REVERT: B  197 ARG cc_start: 0.6587 (mpt180) cc_final: 0.6367 (mpt180)
REVERT: B  228 ASP cc_start: 0.6776 (m-30) cc_final: 0.6542 (m-30)
REVERT: B  246 ASP cc_start: 0.6667 (t70) cc_final: 0.6343 (t70)
REVERT: B  247 ASP cc_start: 0.6195 (t0) cc_final: 0.5826 (t0)
REVERT: B  314 ARG cc_start: 0.6975 (mtp85) cc_final: 0.6699 (mtp85)
REVERT: B  325 MET cc_start: 0.6220 (mpp) cc_final: 0.5658 (mpp)
REVERT: C   52 MET cc_start: 0.7227 (tpt) cc_final: 0.6803 (tpt)
REVERT: R  129 LEU cc_start: 0.7409 (tp) cc_final: 0.7165 (tp)
REVERT: R  131 ILE cc_start: 0.8303 (mp) cc_final: 0.8084 (mp)
REVERT: R  187 MET cc_start: 0.4502 (pmm) cc_final: 0.3565 (pmm)
REVERT: R  289 ASN cc_start: 0.5309 (t0) cc_final: 0.3915 (t0)
REVERT: S   57 THR cc_start: 0.7925 (p) cc_final: 0.7721 (p)
REVERT: S  118 THR cc_start: 0.7889 (p) cc_final: 0.7643 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 271
  average time/residue: 0.1021
  time to fit residues: 37.2567
Evaluate side-chains
  259 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0070
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    0.6980
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
A 241 ASN
A 304 GLN
B  88 ASN
** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.187974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.161026 restraints weight = 13602.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.4002 rms_B_bonded: 2.86
r_work: 0.3869 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6722
moved from start:          0.1076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9289  Z= 0.170
  Angle     :  0.642   7.495  12586  Z= 0.341
  Chirality :  0.044   0.210   1421
  Planarity :  0.005   0.067   1590
  Dihedral  :  4.901  27.208   1261
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.09 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  9.17 %
    Favored  : 89.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.83 (0.24), residues: 1142
  helix:  1.08 (0.27), residues: 374
  sheet:  0.04 (0.32), residues: 260
  loop : -2.20 (0.25), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 283 
 TYR   0.046   0.002   TYR R 114 
 PHE   0.016   0.002   PHE B 278 
 TRP   0.010   0.001   TRP B 211 
 HIS   0.004   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 9288)
  covalent geometry    : angle       0.64159 (12584)
  SS BOND              : bond        0.00239 (    1)
  SS BOND              : angle       0.49916 (    2)
  hydrogen bonds       : bond        0.04549 (  406)
  hydrogen bonds       : angle       5.21081 ( 1161)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 270
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.8037 (mptt) cc_final: 0.7385 (mptt)
REVERT: A   53 MET cc_start: 0.5906 (mmm) cc_final: 0.5641 (mmm)
REVERT: A  194 LEU cc_start: 0.8033 (tp) cc_final: 0.7701 (tp)
REVERT: A  262 THR cc_start: 0.8531 (m) cc_final: 0.8151 (m)
REVERT: A  270 LYS cc_start: 0.7957 (mppt) cc_final: 0.7443 (mppt)
REVERT: A  333 GLN cc_start: 0.8166 (tp40) cc_final: 0.7516 (tp40)
REVERT: A  336 PHE cc_start: 0.7973 (t80) cc_final: 0.7660 (t80)
REVERT: A  349 LYS cc_start: 0.8233 (mttm) cc_final: 0.7895 (mttm)
REVERT: B   46 ARG cc_start: 0.7174 (ptt-90) cc_final: 0.6698 (ptt-90)
REVERT: B   48 ARG cc_start: 0.7687 (mmm160) cc_final: 0.6660 (mmm160)
REVERT: B   61 MET cc_start: 0.7615 (ppp) cc_final: 0.7365 (ppp)
REVERT: B  120 ILE cc_start: 0.8143 (pt) cc_final: 0.7779 (mt)
REVERT: B  155 ASN cc_start: 0.7706 (t0) cc_final: 0.7320 (t0)
REVERT: B  228 ASP cc_start: 0.7177 (m-30) cc_final: 0.6935 (m-30)
REVERT: B  246 ASP cc_start: 0.7363 (t70) cc_final: 0.7018 (t70)
REVERT: B  247 ASP cc_start: 0.7080 (t0) cc_final: 0.6588 (t0)
REVERT: B  314 ARG cc_start: 0.7379 (mtp85) cc_final: 0.7119 (mtp85)
REVERT: B  325 MET cc_start: 0.6974 (mpp) cc_final: 0.6431 (mpp)
REVERT: C   52 MET cc_start: 0.7983 (tpt) cc_final: 0.7397 (tpt)
REVERT: C   61 VAL cc_start: 0.7856 (t) cc_final: 0.7568 (p)
REVERT: C   69 MET cc_start: 0.6573 (mpp) cc_final: 0.6350 (mpp)
REVERT: R  131 ILE cc_start: 0.8389 (mp) cc_final: 0.8071 (mp)
REVERT: R  165 MET cc_start: 0.2550 (mmm) cc_final: 0.2261 (mmm)
REVERT: R  187 MET cc_start: 0.4364 (pmm) cc_final: 0.3528 (pmm)
REVERT: R  246 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6503 (tt)
REVERT: R  250 ILE cc_start: 0.8081 (mp) cc_final: 0.7732 (mp)
REVERT: R  289 ASN cc_start: 0.5640 (t0) cc_final: 0.5056 (t0)
REVERT: R  293 TYR cc_start: 0.7040 (m-80) cc_final: 0.6753 (m-80)
REVERT: S   52 SER cc_start: 0.8313 (t) cc_final: 0.8040 (p)
REVERT: S   57 THR cc_start: 0.8131 (p) cc_final: 0.7881 (p)
REVERT: S   80 PHE cc_start: 0.7964 (m-80) cc_final: 0.7533 (m-80)
REVERT: S  116 THR cc_start: 0.8134 (p) cc_final: 0.7928 (t)
  outliers start: 10
  outliers final: 6
  residues processed: 274
  average time/residue: 0.1002
  time to fit residues: 37.3009
Evaluate side-chains
  278 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 271
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  162 MET
Chi-restraints excluded: chain R residue  246 LEU
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  199 VAL
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 57 optimal weight:    0.8980
   chunk 89 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 30 optimal weight:    0.3980
   chunk 103 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 132 ASN
** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.187863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.160743 restraints weight = 13547.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3995 rms_B_bonded: 2.88
r_work: 0.3860 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6736
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9289  Z= 0.177
  Angle     :  0.617   7.522  12586  Z= 0.326
  Chirality :  0.044   0.193   1421
  Planarity :  0.005   0.065   1590
  Dihedral  :  4.953  33.727   1261
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.74 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 13.41 %
    Favored  : 84.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.24), residues: 1142
  helix:  1.17 (0.27), residues: 374
  sheet:  0.00 (0.32), residues: 261
  loop : -2.11 (0.25), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 283 
 TYR   0.047   0.002   TYR R 114 
 PHE   0.018   0.002   PHE B 278 
 TRP   0.012   0.001   TRP B 211 
 HIS   0.004   0.001   HIS D  26 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 9288)
  covalent geometry    : angle       0.61698 (12584)
  SS BOND              : bond        0.00167 (    1)
  SS BOND              : angle       0.33983 (    2)
  hydrogen bonds       : bond        0.04352 (  406)
  hydrogen bonds       : angle       4.96017 ( 1161)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 264
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.8027 (mptt) cc_final: 0.7355 (mptt)
REVERT: A   53 MET cc_start: 0.5808 (mmm) cc_final: 0.5545 (mmm)
REVERT: A  194 LEU cc_start: 0.8017 (tp) cc_final: 0.7699 (tp)
REVERT: A  240 MET cc_start: 0.6910 (mtp) cc_final: 0.6676 (mtp)
REVERT: A  270 LYS cc_start: 0.7954 (mppt) cc_final: 0.7464 (mppt)
REVERT: A  271 LYS cc_start: 0.7535 (tttt) cc_final: 0.7125 (mttt)
REVERT: A  333 GLN cc_start: 0.8148 (tp40) cc_final: 0.7488 (tp40)
REVERT: A  348 LEU cc_start: 0.8521 (mm) cc_final: 0.8266 (mm)
REVERT: A  349 LYS cc_start: 0.8216 (mttm) cc_final: 0.7900 (mttm)
REVERT: B   22 ARG cc_start: 0.7147 (ptp-110) cc_final: 0.6726 (ptp-110)
REVERT: B   46 ARG cc_start: 0.7227 (ptt-90) cc_final: 0.6710 (ptt-90)
REVERT: B   47 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8163 (m)
REVERT: B   48 ARG cc_start: 0.7785 (mmm160) cc_final: 0.6725 (mmm160)
REVERT: B  120 ILE cc_start: 0.8176 (pt) cc_final: 0.7886 (mt)
REVERT: B  155 ASN cc_start: 0.7785 (t0) cc_final: 0.7413 (t0)
REVERT: B  204 CYS cc_start: 0.8082 (p) cc_final: 0.7160 (p)
REVERT: B  228 ASP cc_start: 0.7254 (m-30) cc_final: 0.6975 (m-30)
REVERT: B  232 ILE cc_start: 0.8411 (mt) cc_final: 0.8112 (tp)
REVERT: B  246 ASP cc_start: 0.7381 (t70) cc_final: 0.7035 (t70)
REVERT: B  247 ASP cc_start: 0.7134 (t0) cc_final: 0.6585 (t0)
REVERT: B  323 ASP cc_start: 0.7334 (t0) cc_final: 0.7067 (t0)
REVERT: B  325 MET cc_start: 0.7175 (mpp) cc_final: 0.6309 (mpp)
REVERT: C   52 MET cc_start: 0.8000 (tpt) cc_final: 0.7435 (tpt)
REVERT: C   69 MET cc_start: 0.6616 (mpp) cc_final: 0.6292 (mpp)
REVERT: R  127 ARG cc_start: 0.7279 (mtt180) cc_final: 0.6824 (mtt180)
REVERT: R  131 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8007 (mp)
REVERT: R  183 MET cc_start: 0.5065 (mtt) cc_final: 0.4770 (mtt)
REVERT: R  187 MET cc_start: 0.4393 (pmm) cc_final: 0.4026 (pmm)
REVERT: R  245 ARG cc_start: 0.6251 (ptt180) cc_final: 0.6031 (ptt180)
REVERT: R  250 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7720 (mp)
REVERT: R  289 ASN cc_start: 0.5646 (t0) cc_final: 0.4758 (t0)
REVERT: R  293 TYR cc_start: 0.7107 (m-80) cc_final: 0.6784 (m-80)
REVERT: S   39 GLN cc_start: 0.8145 (tt0) cc_final: 0.7925 (tp40)
REVERT: S   52 SER cc_start: 0.8337 (t) cc_final: 0.7845 (p)
REVERT: S   80 PHE cc_start: 0.7854 (m-80) cc_final: 0.7523 (m-80)
  outliers start: 18
  outliers final: 7
  residues processed: 271
  average time/residue: 0.0978
  time to fit residues: 36.2052
Evaluate side-chains
  264 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 254
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  131 ILE
Chi-restraints excluded: chain R residue  162 MET
Chi-restraints excluded: chain R residue  250 ILE
Chi-restraints excluded: chain S residue   31 SER
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  174 LEU
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 111 optimal weight:    0.0070
   chunk 9 optimal weight:    1.9990
   chunk 87 optimal weight:    0.6980
   chunk 25 optimal weight:    4.9990
   chunk 94 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   chunk 88 optimal weight:    0.1980
   chunk 42 optimal weight:    0.2980
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.4198

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
** R 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.188980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.161785 restraints weight = 13780.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.4002 rms_B_bonded: 2.92
r_work: 0.3867 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6714
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9289  Z= 0.133
  Angle     :  0.598   8.109  12586  Z= 0.316
  Chirality :  0.043   0.188   1421
  Planarity :  0.004   0.062   1590
  Dihedral  :  4.796  31.959   1261
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.13 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 15.42 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.67 (0.24), residues: 1142
  helix:  1.30 (0.27), residues: 375
  sheet: -0.02 (0.32), residues: 250
  loop : -2.06 (0.25), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 283 
 TYR   0.047   0.002   TYR R 114 
 PHE   0.026   0.002   PHE A 336 
 TRP   0.009   0.001   TRP R 195 
 HIS   0.003   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 9288)
  covalent geometry    : angle       0.59790 (12584)
  SS BOND              : bond        0.00307 (    1)
  SS BOND              : angle       1.48532 (    2)
  hydrogen bonds       : bond        0.04015 (  406)
  hydrogen bonds       : angle       4.82683 ( 1161)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 268
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.8006 (mptt) cc_final: 0.7302 (mptt)
REVERT: A   53 MET cc_start: 0.5821 (mmm) cc_final: 0.5617 (mmm)
REVERT: A  194 LEU cc_start: 0.7977 (tp) cc_final: 0.7686 (tp)
REVERT: A  243 MET cc_start: 0.7445 (tpp) cc_final: 0.7243 (tpp)
REVERT: A  270 LYS cc_start: 0.7861 (mppt) cc_final: 0.7366 (mppt)
REVERT: A  271 LYS cc_start: 0.7458 (tttt) cc_final: 0.7063 (mttt)
REVERT: A  333 GLN cc_start: 0.8167 (tp40) cc_final: 0.7494 (tp40)
REVERT: A  349 LYS cc_start: 0.8214 (mttm) cc_final: 0.7896 (mttm)
REVERT: B   22 ARG cc_start: 0.7038 (ptp-110) cc_final: 0.6766 (ptp-170)
REVERT: B   46 ARG cc_start: 0.7276 (ptt-90) cc_final: 0.6777 (ptt-90)
REVERT: B   47 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8150 (m)
REVERT: B   68 ARG cc_start: 0.8135 (ttt-90) cc_final: 0.7765 (ttt-90)
REVERT: B   83 ASP cc_start: 0.7896 (t0) cc_final: 0.7491 (t0)
REVERT: B   86 THR cc_start: 0.8195 (p) cc_final: 0.7898 (p)
REVERT: B   88 ASN cc_start: 0.8025 (m110) cc_final: 0.7633 (m-40)
REVERT: B   97 SER cc_start: 0.8260 (t) cc_final: 0.7972 (p)
REVERT: B  120 ILE cc_start: 0.8132 (pt) cc_final: 0.7885 (mt)
REVERT: B  132 ASN cc_start: 0.7209 (p0) cc_final: 0.6968 (p0)
REVERT: B  155 ASN cc_start: 0.7784 (t0) cc_final: 0.7374 (t0)
REVERT: B  175 GLN cc_start: 0.7207 (mp10) cc_final: 0.6854 (mp10)
REVERT: B  204 CYS cc_start: 0.8035 (p) cc_final: 0.7069 (p)
REVERT: B  228 ASP cc_start: 0.7303 (m-30) cc_final: 0.6985 (m-30)
REVERT: B  232 ILE cc_start: 0.8386 (mt) cc_final: 0.8106 (tp)
REVERT: B  246 ASP cc_start: 0.7404 (t70) cc_final: 0.7050 (t70)
REVERT: B  314 ARG cc_start: 0.7475 (mtp85) cc_final: 0.7274 (mtp85)
REVERT: B  323 ASP cc_start: 0.7284 (t0) cc_final: 0.7046 (t0)
REVERT: B  325 MET cc_start: 0.7140 (mpp) cc_final: 0.6171 (mpp)
REVERT: C   52 MET cc_start: 0.7998 (tpt) cc_final: 0.7435 (tpt)
REVERT: C   69 MET cc_start: 0.6578 (mpp) cc_final: 0.6221 (mpp)
REVERT: R  127 ARG cc_start: 0.7231 (mtt180) cc_final: 0.6788 (mtt180)
REVERT: R  131 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.7980 (mp)
REVERT: R  187 MET cc_start: 0.5560 (pmm) cc_final: 0.4869 (pmm)
REVERT: R  245 ARG cc_start: 0.6277 (ptt180) cc_final: 0.6035 (ptt180)
REVERT: R  246 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6490 (tt)
REVERT: R  250 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7761 (mp)
REVERT: R  289 ASN cc_start: 0.5637 (t0) cc_final: 0.4556 (t0)
REVERT: R  293 TYR cc_start: 0.6995 (m-80) cc_final: 0.6677 (m-80)
REVERT: S   52 SER cc_start: 0.8411 (t) cc_final: 0.8078 (p)
REVERT: S   80 PHE cc_start: 0.7785 (m-80) cc_final: 0.7477 (m-80)
  outliers start: 19
  outliers final: 8
  residues processed: 278
  average time/residue: 0.1034
  time to fit residues: 39.0356
Evaluate side-chains
  278 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 266
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  131 ILE
Chi-restraints excluded: chain R residue  162 MET
Chi-restraints excluded: chain R residue  246 LEU
Chi-restraints excluded: chain R residue  250 ILE
Chi-restraints excluded: chain S residue   31 SER
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0070
   chunk 58 optimal weight:    0.6980
   chunk 52 optimal weight:    4.9990
   chunk 1 optimal weight:    0.4980
   chunk 40 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 18 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.5798

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

Flipped N/Q/H residues before XYZ refinement:
** R 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.188723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.161491 restraints weight = 13597.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.4002 rms_B_bonded: 2.87
r_work: 0.3867 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6728
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9289  Z= 0.149
  Angle     :  0.602   8.277  12586  Z= 0.317
  Chirality :  0.043   0.185   1421
  Planarity :  0.004   0.061   1590
  Dihedral  :  4.800  32.971   1261
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.83 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 16.63 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.62 (0.25), residues: 1142
  helix:  1.34 (0.27), residues: 375
  sheet: -0.05 (0.32), residues: 258
  loop : -2.03 (0.25), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 283 
 TYR   0.048   0.002   TYR R 114 
 PHE   0.018   0.001   PHE A 336 
 TRP   0.012   0.001   TRP A 258 
 HIS   0.003   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 9288)
  covalent geometry    : angle       0.60165 (12584)
  SS BOND              : bond        0.00425 (    1)
  SS BOND              : angle       1.10234 (    2)
  hydrogen bonds       : bond        0.04016 (  406)
  hydrogen bonds       : angle       4.77269 ( 1161)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 267
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.7986 (mptt) cc_final: 0.7264 (mptt)
REVERT: A  194 LEU cc_start: 0.7987 (tp) cc_final: 0.7709 (tp)
REVERT: A  243 MET cc_start: 0.7448 (tpp) cc_final: 0.7211 (tpp)
REVERT: A  270 LYS cc_start: 0.7845 (mppt) cc_final: 0.7336 (mppt)
REVERT: A  271 LYS cc_start: 0.7455 (tttt) cc_final: 0.7071 (mttt)
REVERT: A  333 GLN cc_start: 0.8172 (tp40) cc_final: 0.7511 (tp40)
REVERT: A  349 LYS cc_start: 0.8212 (mttm) cc_final: 0.7892 (mttm)
REVERT: B   22 ARG cc_start: 0.7105 (ptp-110) cc_final: 0.6843 (ptp-170)
REVERT: B   46 ARG cc_start: 0.7222 (ptt-90) cc_final: 0.6819 (ptt-90)
REVERT: B   47 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8154 (m)
REVERT: B   68 ARG cc_start: 0.8198 (ttt-90) cc_final: 0.7800 (ttt-90)
REVERT: B   83 ASP cc_start: 0.7945 (t0) cc_final: 0.7514 (t0)
REVERT: B   86 THR cc_start: 0.8208 (p) cc_final: 0.7892 (p)
REVERT: B   88 ASN cc_start: 0.8000 (m110) cc_final: 0.7626 (m-40)
REVERT: B   97 SER cc_start: 0.8278 (t) cc_final: 0.7997 (p)
REVERT: B  120 ILE cc_start: 0.8094 (pt) cc_final: 0.7873 (mt)
REVERT: B  132 ASN cc_start: 0.7237 (p0) cc_final: 0.7007 (p0)
REVERT: B  155 ASN cc_start: 0.7824 (t0) cc_final: 0.7424 (t0)
REVERT: B  175 GLN cc_start: 0.7187 (mp10) cc_final: 0.6807 (mp10)
REVERT: B  204 CYS cc_start: 0.8049 (p) cc_final: 0.7072 (p)
REVERT: B  228 ASP cc_start: 0.7269 (m-30) cc_final: 0.6913 (m-30)
REVERT: B  230 ASN cc_start: 0.7894 (m-40) cc_final: 0.7617 (m110)
REVERT: B  232 ILE cc_start: 0.8393 (mt) cc_final: 0.8128 (tp)
REVERT: B  246 ASP cc_start: 0.7429 (t70) cc_final: 0.7075 (t70)
REVERT: B  293 ASN cc_start: 0.8408 (p0) cc_final: 0.8157 (p0)
REVERT: B  325 MET cc_start: 0.7196 (mpp) cc_final: 0.6372 (mpp)
REVERT: C   52 MET cc_start: 0.7996 (tpt) cc_final: 0.7445 (tpt)
REVERT: C   69 MET cc_start: 0.6582 (mpp) cc_final: 0.6202 (mpp)
REVERT: R  127 ARG cc_start: 0.7251 (mtt180) cc_final: 0.6777 (mtt180)
REVERT: R  131 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8006 (mp)
REVERT: R  183 MET cc_start: 0.5137 (mtt) cc_final: 0.4733 (mtt)
REVERT: R  187 MET cc_start: 0.5461 (pmm) cc_final: 0.4682 (pmm)
REVERT: R  245 ARG cc_start: 0.6249 (ptt180) cc_final: 0.6011 (ptt180)
REVERT: R  246 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6492 (tt)
REVERT: R  250 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7755 (mp)
REVERT: R  289 ASN cc_start: 0.5585 (t0) cc_final: 0.4476 (t0)
REVERT: R  293 TYR cc_start: 0.7010 (m-80) cc_final: 0.6719 (m-80)
REVERT: S   52 SER cc_start: 0.8362 (t) cc_final: 0.8127 (p)
REVERT: S   80 PHE cc_start: 0.7801 (m-80) cc_final: 0.7491 (m-80)
  outliers start: 21
  outliers final: 10
  residues processed: 277
  average time/residue: 0.0989
  time to fit residues: 37.5124
Evaluate side-chains
  272 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 258
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  131 ILE
Chi-restraints excluded: chain R residue  162 MET
Chi-restraints excluded: chain R residue  246 LEU
Chi-restraints excluded: chain R residue  250 ILE
Chi-restraints excluded: chain S residue   31 SER
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  174 LEU
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 66 optimal weight:    0.8980
   chunk 61 optimal weight:    4.9990
   chunk 79 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 69 optimal weight:    0.7980
   chunk 82 optimal weight:    1.9990
   chunk 34 optimal weight:    0.3980
   chunk 47 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.7380

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.188562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.160894 restraints weight = 13578.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.3995 rms_B_bonded: 2.90
r_work: 0.3860 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6744
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9289  Z= 0.171
  Angle     :  0.630   8.342  12586  Z= 0.329
  Chirality :  0.044   0.187   1421
  Planarity :  0.005   0.060   1590
  Dihedral  :  4.862  34.159   1261
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.22 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 17.94 %
    Favored  : 80.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.69 (0.24), residues: 1142
  helix:  1.29 (0.27), residues: 373
  sheet: -0.09 (0.32), residues: 258
  loop : -2.06 (0.25), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 283 
 TYR   0.050   0.002   TYR R 114 
 PHE   0.016   0.002   PHE B 278 
 TRP   0.009   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 9288)
  covalent geometry    : angle       0.63002 (12584)
  SS BOND              : bond        0.00131 (    1)
  SS BOND              : angle       1.16311 (    2)
  hydrogen bonds       : bond        0.04096 (  406)
  hydrogen bonds       : angle       4.75994 ( 1161)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 259
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.7963 (mptt) cc_final: 0.7231 (mptt)
REVERT: A  194 LEU cc_start: 0.7983 (tp) cc_final: 0.7698 (tp)
REVERT: A  270 LYS cc_start: 0.7856 (mppt) cc_final: 0.7344 (mppt)
REVERT: A  271 LYS cc_start: 0.7467 (tttt) cc_final: 0.7137 (mttt)
REVERT: A  312 LYS cc_start: 0.8159 (mmtt) cc_final: 0.7913 (mmtt)
REVERT: A  333 GLN cc_start: 0.8176 (tp40) cc_final: 0.7548 (tp40)
REVERT: A  349 LYS cc_start: 0.8230 (mttm) cc_final: 0.7908 (mttm)
REVERT: B   22 ARG cc_start: 0.7163 (ptp-110) cc_final: 0.6916 (ptp-170)
REVERT: B   32 GLN cc_start: 0.7521 (tp40) cc_final: 0.7222 (tp40)
REVERT: B   46 ARG cc_start: 0.7252 (ptt-90) cc_final: 0.6915 (ptt-90)
REVERT: B   47 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8192 (m)
REVERT: B   68 ARG cc_start: 0.8220 (ttt-90) cc_final: 0.7780 (ttt-90)
REVERT: B   83 ASP cc_start: 0.7944 (t0) cc_final: 0.7484 (t0)
REVERT: B   86 THR cc_start: 0.8322 (p) cc_final: 0.7973 (p)
REVERT: B   88 ASN cc_start: 0.8044 (m110) cc_final: 0.7649 (m-40)
REVERT: B   97 SER cc_start: 0.8272 (t) cc_final: 0.7961 (p)
REVERT: B  132 ASN cc_start: 0.7169 (p0) cc_final: 0.6944 (p0)
REVERT: B  155 ASN cc_start: 0.7837 (t0) cc_final: 0.7426 (t0)
REVERT: B  175 GLN cc_start: 0.7185 (mp10) cc_final: 0.6805 (mp10)
REVERT: B  204 CYS cc_start: 0.8054 (p) cc_final: 0.7134 (p)
REVERT: B  228 ASP cc_start: 0.7290 (m-30) cc_final: 0.6927 (m-30)
REVERT: B  230 ASN cc_start: 0.7936 (m-40) cc_final: 0.7675 (m110)
REVERT: B  232 ILE cc_start: 0.8365 (mt) cc_final: 0.8108 (tp)
REVERT: B  246 ASP cc_start: 0.7448 (t70) cc_final: 0.7095 (t70)
REVERT: B  293 ASN cc_start: 0.8461 (p0) cc_final: 0.8115 (p0)
REVERT: B  314 ARG cc_start: 0.7512 (mtp85) cc_final: 0.7265 (mtp85)
REVERT: B  325 MET cc_start: 0.7267 (mpp) cc_final: 0.6568 (mpp)
REVERT: C   52 MET cc_start: 0.8014 (tpt) cc_final: 0.7470 (tpt)
REVERT: C   69 MET cc_start: 0.6619 (mpp) cc_final: 0.6095 (mpp)
REVERT: R  127 ARG cc_start: 0.7305 (mtt180) cc_final: 0.6830 (mtt180)
REVERT: R  131 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.7986 (mp)
REVERT: R  178 LYS cc_start: 0.8282 (mppt) cc_final: 0.8061 (mppt)
REVERT: R  183 MET cc_start: 0.5203 (mtt) cc_final: 0.4176 (mtt)
REVERT: R  187 MET cc_start: 0.5680 (OUTLIER) cc_final: 0.4885 (pmm)
REVERT: R  245 ARG cc_start: 0.6214 (ptt180) cc_final: 0.5965 (ptt180)
REVERT: R  246 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6516 (tp)
REVERT: R  250 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7778 (mp)
REVERT: R  289 ASN cc_start: 0.5634 (t0) cc_final: 0.4566 (t0)
REVERT: R  293 TYR cc_start: 0.7001 (m-80) cc_final: 0.6723 (m-80)
REVERT: S   52 SER cc_start: 0.8370 (t) cc_final: 0.8123 (p)
REVERT: S   78 THR cc_start: 0.8393 (m) cc_final: 0.7852 (t)
REVERT: S   80 PHE cc_start: 0.7832 (m-80) cc_final: 0.7336 (m-80)
REVERT: S  234 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.5929 (pp20)
REVERT: D   26 HIS cc_start: 0.6003 (OUTLIER) cc_final: 0.4786 (t70)
  outliers start: 20
  outliers final: 9
  residues processed: 272
  average time/residue: 0.1032
  time to fit residues: 38.1599
Evaluate side-chains
  273 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 257
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  131 ILE
Chi-restraints excluded: chain R residue  187 MET
Chi-restraints excluded: chain R residue  246 LEU
Chi-restraints excluded: chain R residue  250 ILE
Chi-restraints excluded: chain S residue   31 SER
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  174 LEU
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain S residue  233 LEU
Chi-restraints excluded: chain S residue  234 GLU
Chi-restraints excluded: chain D residue   26 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 103 optimal weight:    0.0470
   chunk 40 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0020
   chunk 69 optimal weight:    0.9980
   chunk 112 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.5086

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN
** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.189278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.162369 restraints weight = 13825.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.4008 rms_B_bonded: 2.91
r_work: 0.3872 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6725
moved from start:          0.2040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9289  Z= 0.145
  Angle     :  0.628   8.694  12586  Z= 0.329
  Chirality :  0.043   0.199   1421
  Planarity :  0.005   0.061   1590
  Dihedral  :  4.828  34.254   1261
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.13 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 18.65 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.64 (0.25), residues: 1142
  helix:  1.35 (0.27), residues: 375
  sheet: -0.06 (0.32), residues: 253
  loop : -2.04 (0.25), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 283 
 TYR   0.047   0.002   TYR R 114 
 PHE   0.035   0.002   PHE A 336 
 TRP   0.009   0.001   TRP B 211 
 HIS   0.002   0.001   HIS D  26 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 9288)
  covalent geometry    : angle       0.62600 (12584)
  SS BOND              : bond        0.00290 (    1)
  SS BOND              : angle       3.68127 (    2)
  hydrogen bonds       : bond        0.03951 (  406)
  hydrogen bonds       : angle       4.73711 ( 1161)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 254
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.7976 (mptt) cc_final: 0.7235 (mptt)
REVERT: A  194 LEU cc_start: 0.7993 (tp) cc_final: 0.7719 (tp)
REVERT: A  243 MET cc_start: 0.7457 (tpp) cc_final: 0.7186 (tpp)
REVERT: A  270 LYS cc_start: 0.7865 (mppt) cc_final: 0.7337 (mppt)
REVERT: A  271 LYS cc_start: 0.7440 (tttt) cc_final: 0.7045 (mttt)
REVERT: A  312 LYS cc_start: 0.8172 (mmtt) cc_final: 0.7926 (mmtt)
REVERT: A  333 GLN cc_start: 0.8172 (tp40) cc_final: 0.7526 (tp40)
REVERT: A  349 LYS cc_start: 0.8185 (mttm) cc_final: 0.7857 (mttm)
REVERT: B   22 ARG cc_start: 0.7074 (ptp-110) cc_final: 0.6849 (ptp-170)
REVERT: B   32 GLN cc_start: 0.7540 (tp40) cc_final: 0.7243 (tp40)
REVERT: B   46 ARG cc_start: 0.7241 (ptt-90) cc_final: 0.6946 (ptt-90)
REVERT: B   68 ARG cc_start: 0.8191 (ttt-90) cc_final: 0.7744 (ttt-90)
REVERT: B   86 THR cc_start: 0.8299 (p) cc_final: 0.7975 (p)
REVERT: B   88 ASN cc_start: 0.8047 (m110) cc_final: 0.7678 (m-40)
REVERT: B   97 SER cc_start: 0.8271 (t) cc_final: 0.7984 (p)
REVERT: B  132 ASN cc_start: 0.7119 (p0) cc_final: 0.6898 (p0)
REVERT: B  155 ASN cc_start: 0.7830 (t0) cc_final: 0.7411 (t0)
REVERT: B  175 GLN cc_start: 0.7155 (mp10) cc_final: 0.6737 (mp10)
REVERT: B  204 CYS cc_start: 0.8028 (p) cc_final: 0.7075 (p)
REVERT: B  228 ASP cc_start: 0.7365 (m-30) cc_final: 0.6965 (m-30)
REVERT: B  230 ASN cc_start: 0.7907 (m-40) cc_final: 0.7616 (m110)
REVERT: B  232 ILE cc_start: 0.8377 (mt) cc_final: 0.8108 (tp)
REVERT: B  246 ASP cc_start: 0.7448 (t70) cc_final: 0.7094 (t70)
REVERT: B  325 MET cc_start: 0.7300 (mpp) cc_final: 0.6587 (mpp)
REVERT: C   52 MET cc_start: 0.8030 (tpt) cc_final: 0.7488 (tpt)
REVERT: C   69 MET cc_start: 0.6617 (mpp) cc_final: 0.6096 (mpp)
REVERT: R  131 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.7975 (mp)
REVERT: R  187 MET cc_start: 0.5711 (pmm) cc_final: 0.4935 (pmm)
REVERT: R  245 ARG cc_start: 0.6231 (ptt180) cc_final: 0.5916 (ppt170)
REVERT: R  246 LEU cc_start: 0.6819 (OUTLIER) cc_final: 0.6484 (tt)
REVERT: R  250 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7773 (mp)
REVERT: R  289 ASN cc_start: 0.5576 (t0) cc_final: 0.4470 (t0)
REVERT: R  293 TYR cc_start: 0.7004 (m-80) cc_final: 0.6701 (m-80)
REVERT: S   52 SER cc_start: 0.8347 (t) cc_final: 0.8092 (p)
REVERT: S   78 THR cc_start: 0.8403 (m) cc_final: 0.7856 (t)
REVERT: S   80 PHE cc_start: 0.7726 (m-80) cc_final: 0.7277 (m-80)
REVERT: S  234 GLU cc_start: 0.6365 (OUTLIER) cc_final: 0.5923 (pp20)
REVERT: D   26 HIS cc_start: 0.5988 (OUTLIER) cc_final: 0.5343 (t70)
  outliers start: 20
  outliers final: 12
  residues processed: 268
  average time/residue: 0.1074
  time to fit residues: 38.7478
Evaluate side-chains
  270 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 253
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   31 ILE
Chi-restraints excluded: chain R residue  131 ILE
Chi-restraints excluded: chain R residue  181 CYS
Chi-restraints excluded: chain R residue  246 LEU
Chi-restraints excluded: chain R residue  250 ILE
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  174 LEU
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain S residue  233 LEU
Chi-restraints excluded: chain S residue  234 GLU
Chi-restraints excluded: chain D residue   26 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 108 optimal weight:    2.9990
   chunk 110 optimal weight:    1.9990
   chunk 100 optimal weight:    0.3980
   chunk 62 optimal weight:   40.0000
   chunk 92 optimal weight:    0.9990
   chunk 95 optimal weight:    0.0470
   chunk 52 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.6282

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.188671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.161914 restraints weight = 13703.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.4001 rms_B_bonded: 2.89
r_work: 0.3865 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6735
moved from start:          0.2140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9289  Z= 0.158
  Angle     :  0.651   8.722  12586  Z= 0.338
  Chirality :  0.044   0.199   1421
  Planarity :  0.005   0.060   1590
  Dihedral  :  4.862  35.280   1261
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.65 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 19.15 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.67 (0.25), residues: 1142
  helix:  1.30 (0.27), residues: 375
  sheet: -0.13 (0.32), residues: 255
  loop : -2.01 (0.26), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 314 
 TYR   0.046   0.002   TYR R 114 
 PHE   0.031   0.002   PHE A 336 
 TRP   0.008   0.001   TRP B 211 
 HIS   0.003   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 9288)
  covalent geometry    : angle       0.64903 (12584)
  SS BOND              : bond        0.00328 (    1)
  SS BOND              : angle       3.98527 (    2)
  hydrogen bonds       : bond        0.03983 (  406)
  hydrogen bonds       : angle       4.74888 ( 1161)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 253
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 LEU cc_start: 0.8000 (tp) cc_final: 0.7719 (tp)
REVERT: A  243 MET cc_start: 0.7470 (tpp) cc_final: 0.7157 (tpp)
REVERT: A  270 LYS cc_start: 0.7880 (mppt) cc_final: 0.7354 (mppt)
REVERT: A  271 LYS cc_start: 0.7466 (tttt) cc_final: 0.7137 (mttt)
REVERT: A  312 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7937 (mmtt)
REVERT: A  333 GLN cc_start: 0.8178 (tp40) cc_final: 0.7537 (tp40)
REVERT: A  349 LYS cc_start: 0.8188 (mttm) cc_final: 0.7852 (mttm)
REVERT: B   22 ARG cc_start: 0.7074 (ptp-110) cc_final: 0.6863 (ptp-170)
REVERT: B   32 GLN cc_start: 0.7500 (tp40) cc_final: 0.7205 (tp40)
REVERT: B   46 ARG cc_start: 0.7261 (ptt-90) cc_final: 0.6989 (ptt-90)
REVERT: B   68 ARG cc_start: 0.8222 (ttt-90) cc_final: 0.7765 (ttt-90)
REVERT: B   83 ASP cc_start: 0.7934 (t0) cc_final: 0.7446 (t0)
REVERT: B   86 THR cc_start: 0.8372 (p) cc_final: 0.7986 (p)
REVERT: B   88 ASN cc_start: 0.8091 (m110) cc_final: 0.7686 (m-40)
REVERT: B   97 SER cc_start: 0.8272 (t) cc_final: 0.7964 (p)
REVERT: B  132 ASN cc_start: 0.7175 (p0) cc_final: 0.6952 (p0)
REVERT: B  143 THR cc_start: 0.8310 (t) cc_final: 0.8088 (p)
REVERT: B  155 ASN cc_start: 0.7797 (t0) cc_final: 0.7373 (t0)
REVERT: B  175 GLN cc_start: 0.7172 (mp10) cc_final: 0.6756 (mp10)
REVERT: B  204 CYS cc_start: 0.8087 (p) cc_final: 0.7175 (p)
REVERT: B  228 ASP cc_start: 0.7380 (m-30) cc_final: 0.7043 (m-30)
REVERT: B  232 ILE cc_start: 0.8334 (mt) cc_final: 0.8094 (tp)
REVERT: B  246 ASP cc_start: 0.7463 (t70) cc_final: 0.7109 (t70)
REVERT: B  291 ASP cc_start: 0.7774 (p0) cc_final: 0.7320 (p0)
REVERT: B  293 ASN cc_start: 0.8567 (p0) cc_final: 0.8295 (p0)
REVERT: B  325 MET cc_start: 0.7286 (mpp) cc_final: 0.6581 (mpp)
REVERT: C   52 MET cc_start: 0.8005 (tpt) cc_final: 0.7462 (tpt)
REVERT: C   69 MET cc_start: 0.6565 (OUTLIER) cc_final: 0.6064 (mpp)
REVERT: R  131 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8000 (mp)
REVERT: R  187 MET cc_start: 0.5766 (OUTLIER) cc_final: 0.4983 (pmm)
REVERT: R  245 ARG cc_start: 0.6193 (ptt180) cc_final: 0.5892 (ppt170)
REVERT: R  246 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6494 (tt)
REVERT: R  250 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7791 (mp)
REVERT: R  289 ASN cc_start: 0.5666 (t0) cc_final: 0.4659 (t0)
REVERT: R  293 TYR cc_start: 0.7008 (m-80) cc_final: 0.6728 (m-80)
REVERT: S   52 SER cc_start: 0.8319 (t) cc_final: 0.8091 (p)
REVERT: S   78 THR cc_start: 0.8394 (m) cc_final: 0.7824 (t)
REVERT: S   80 PHE cc_start: 0.7730 (m-80) cc_final: 0.7289 (m-80)
REVERT: S  234 GLU cc_start: 0.6383 (OUTLIER) cc_final: 0.5934 (pp20)
  outliers start: 23
  outliers final: 13
  residues processed: 266
  average time/residue: 0.1087
  time to fit residues: 39.1808
Evaluate side-chains
  269 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 250
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   69 MET
Chi-restraints excluded: chain R residue   31 ILE
Chi-restraints excluded: chain R residue  131 ILE
Chi-restraints excluded: chain R residue  187 MET
Chi-restraints excluded: chain R residue  246 LEU
Chi-restraints excluded: chain R residue  250 ILE
Chi-restraints excluded: chain S residue   31 SER
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  174 LEU
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain S residue  233 LEU
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 105 optimal weight:    0.7980
   chunk 65 optimal weight:    0.5980
   chunk 103 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 63 optimal weight:    0.2980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.188600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.161585 restraints weight = 13609.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.4002 rms_B_bonded: 2.90
r_work: 0.3866 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6731
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9289  Z= 0.160
  Angle     :  0.656   8.770  12586  Z= 0.342
  Chirality :  0.045   0.212   1421
  Planarity :  0.005   0.060   1590
  Dihedral  :  4.881  35.210   1261
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.57 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 19.86 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.70 (0.25), residues: 1142
  helix:  1.27 (0.27), residues: 376
  sheet: -0.10 (0.33), residues: 250
  loop : -2.04 (0.25), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 283 
 TYR   0.046   0.002   TYR R 114 
 PHE   0.029   0.002   PHE A 336 
 TRP   0.009   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 9288)
  covalent geometry    : angle       0.65502 (12584)
  SS BOND              : bond        0.00077 (    1)
  SS BOND              : angle       2.90648 (    2)
  hydrogen bonds       : bond        0.03993 (  406)
  hydrogen bonds       : angle       4.73382 ( 1161)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 251
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  192 LYS cc_start: 0.8290 (mttp) cc_final: 0.8013 (mttp)
REVERT: A  194 LEU cc_start: 0.7992 (tp) cc_final: 0.7715 (tp)
REVERT: A  243 MET cc_start: 0.7484 (tpp) cc_final: 0.7193 (tpp)
REVERT: A  270 LYS cc_start: 0.7853 (mppt) cc_final: 0.7329 (mppt)
REVERT: A  271 LYS cc_start: 0.7417 (tttt) cc_final: 0.7025 (mttt)
REVERT: A  275 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7253 (mt-10)
REVERT: A  312 LYS cc_start: 0.8192 (mmtt) cc_final: 0.7931 (mmtt)
REVERT: A  333 GLN cc_start: 0.8182 (tp40) cc_final: 0.7578 (tp40)
REVERT: A  349 LYS cc_start: 0.8187 (mttm) cc_final: 0.7852 (mttm)
REVERT: B   22 ARG cc_start: 0.7078 (ptp-110) cc_final: 0.6843 (ptp-170)
REVERT: B   32 GLN cc_start: 0.7528 (tp40) cc_final: 0.7231 (tp40)
REVERT: B   46 ARG cc_start: 0.7276 (ptt-90) cc_final: 0.6932 (ptt-90)
REVERT: B   68 ARG cc_start: 0.8213 (ttt-90) cc_final: 0.7736 (ttt-90)
REVERT: B   83 ASP cc_start: 0.7936 (t0) cc_final: 0.7438 (t0)
REVERT: B   86 THR cc_start: 0.8324 (p) cc_final: 0.7919 (p)
REVERT: B   88 ASN cc_start: 0.8085 (m110) cc_final: 0.7665 (m-40)
REVERT: B  132 ASN cc_start: 0.7190 (p0) cc_final: 0.6970 (p0)
REVERT: B  143 THR cc_start: 0.8312 (t) cc_final: 0.8078 (p)
REVERT: B  155 ASN cc_start: 0.7803 (t0) cc_final: 0.7397 (t0)
REVERT: B  175 GLN cc_start: 0.7196 (mp10) cc_final: 0.6781 (mp10)
REVERT: B  204 CYS cc_start: 0.8049 (p) cc_final: 0.7147 (p)
REVERT: B  228 ASP cc_start: 0.7411 (m-30) cc_final: 0.7001 (m-30)
REVERT: B  230 ASN cc_start: 0.7927 (m-40) cc_final: 0.7645 (m110)
REVERT: B  232 ILE cc_start: 0.8374 (mt) cc_final: 0.8108 (tp)
REVERT: B  246 ASP cc_start: 0.7474 (t70) cc_final: 0.7123 (t70)
REVERT: B  293 ASN cc_start: 0.8568 (p0) cc_final: 0.8291 (p0)
REVERT: B  325 MET cc_start: 0.7293 (mpp) cc_final: 0.6685 (mpp)
REVERT: C   52 MET cc_start: 0.7996 (tpt) cc_final: 0.7456 (tpt)
REVERT: C   69 MET cc_start: 0.6616 (OUTLIER) cc_final: 0.6185 (mpp)
REVERT: R  131 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.7979 (mp)
REVERT: R  187 MET cc_start: 0.5725 (OUTLIER) cc_final: 0.4933 (pmm)
REVERT: R  245 ARG cc_start: 0.6218 (ptt180) cc_final: 0.5875 (ppt170)
REVERT: R  246 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6492 (tt)
REVERT: R  250 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7777 (mp)
REVERT: R  289 ASN cc_start: 0.5802 (t0) cc_final: 0.4857 (t0)
REVERT: R  293 TYR cc_start: 0.7062 (m-80) cc_final: 0.6785 (m-80)
REVERT: S   39 GLN cc_start: 0.8196 (tp40) cc_final: 0.7771 (tp40)
REVERT: S   52 SER cc_start: 0.8295 (t) cc_final: 0.8070 (p)
REVERT: S   78 THR cc_start: 0.8389 (m) cc_final: 0.7817 (t)
REVERT: S   80 PHE cc_start: 0.7741 (m-80) cc_final: 0.7281 (m-80)
REVERT: S  234 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.5865 (pp20)
REVERT: D   26 HIS cc_start: 0.5991 (OUTLIER) cc_final: 0.5355 (t70)
  outliers start: 20
  outliers final: 13
  residues processed: 263
  average time/residue: 0.1082
  time to fit residues: 38.4779
Evaluate side-chains
  270 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 250
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   69 MET
Chi-restraints excluded: chain R residue   31 ILE
Chi-restraints excluded: chain R residue  131 ILE
Chi-restraints excluded: chain R residue  181 CYS
Chi-restraints excluded: chain R residue  187 MET
Chi-restraints excluded: chain R residue  246 LEU
Chi-restraints excluded: chain R residue  250 ILE
Chi-restraints excluded: chain S residue   31 SER
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  174 LEU
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain S residue  233 LEU
Chi-restraints excluded: chain S residue  234 GLU
Chi-restraints excluded: chain D residue   26 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 58 optimal weight:    0.4980
   chunk 45 optimal weight:    0.0970
   chunk 55 optimal weight:    0.9980
   chunk 67 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9990
   chunk 62 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.6378

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.188308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.160614 restraints weight = 13619.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.4014 rms_B_bonded: 2.81
r_work: 0.3883 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6749
moved from start:          0.2290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9289  Z= 0.160
  Angle     :  0.660   8.839  12586  Z= 0.343
  Chirality :  0.044   0.190   1421
  Planarity :  0.005   0.060   1590
  Dihedral  :  4.874  35.445   1261
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.01 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 19.96 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.69 (0.25), residues: 1142
  helix:  1.24 (0.27), residues: 378
  sheet: -0.00 (0.33), residues: 246
  loop : -2.06 (0.25), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 283 
 TYR   0.047   0.002   TYR R 114 
 PHE   0.027   0.002   PHE A 336 
 TRP   0.008   0.001   TRP B  63 
 HIS   0.003   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 9288)
  covalent geometry    : angle       0.65974 (12584)
  SS BOND              : bond        0.00002 (    1)
  SS BOND              : angle       2.55971 (    2)
  hydrogen bonds       : bond        0.03989 (  406)
  hydrogen bonds       : angle       4.72869 ( 1161)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 250
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  192 LYS cc_start: 0.8243 (mttp) cc_final: 0.7986 (mttp)
REVERT: A  194 LEU cc_start: 0.8046 (tp) cc_final: 0.7801 (tp)
REVERT: A  270 LYS cc_start: 0.7858 (mppt) cc_final: 0.7369 (mppt)
REVERT: A  271 LYS cc_start: 0.7475 (tttt) cc_final: 0.7177 (mttt)
REVERT: A  312 LYS cc_start: 0.8133 (mmtt) cc_final: 0.7904 (mmtt)
REVERT: A  333 GLN cc_start: 0.8182 (tp40) cc_final: 0.7632 (tp40)
REVERT: A  349 LYS cc_start: 0.8198 (mttm) cc_final: 0.7868 (mttm)
REVERT: B   22 ARG cc_start: 0.7094 (ptp-110) cc_final: 0.6853 (ptp-170)
REVERT: B   32 GLN cc_start: 0.7449 (tp40) cc_final: 0.7184 (tp40)
REVERT: B   46 ARG cc_start: 0.7329 (ptt-90) cc_final: 0.6997 (ptt-90)
REVERT: B   68 ARG cc_start: 0.8205 (ttt-90) cc_final: 0.7774 (ttt-90)
REVERT: B   86 THR cc_start: 0.8389 (p) cc_final: 0.7989 (p)
REVERT: B   88 ASN cc_start: 0.8105 (m110) cc_final: 0.7661 (m-40)
REVERT: B  155 ASN cc_start: 0.7871 (t0) cc_final: 0.7471 (t0)
REVERT: B  175 GLN cc_start: 0.7178 (mp10) cc_final: 0.6789 (mp10)
REVERT: B  204 CYS cc_start: 0.8093 (p) cc_final: 0.7146 (p)
REVERT: B  228 ASP cc_start: 0.7318 (m-30) cc_final: 0.7025 (m-30)
REVERT: B  232 ILE cc_start: 0.8279 (mt) cc_final: 0.8073 (tp)
REVERT: B  246 ASP cc_start: 0.7434 (t70) cc_final: 0.7089 (t70)
REVERT: B  325 MET cc_start: 0.7289 (mpp) cc_final: 0.6776 (mpp)
REVERT: C   52 MET cc_start: 0.7946 (tpt) cc_final: 0.7444 (tpt)
REVERT: C   69 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.6120 (mpp)
REVERT: R  131 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.7992 (mp)
REVERT: R  187 MET cc_start: 0.5710 (OUTLIER) cc_final: 0.4963 (pmm)
REVERT: R  245 ARG cc_start: 0.6097 (ptt180) cc_final: 0.5821 (ppt170)
REVERT: R  246 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6476 (tt)
REVERT: R  250 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7796 (mp)
REVERT: R  289 ASN cc_start: 0.5971 (t0) cc_final: 0.5081 (t0)
REVERT: S   78 THR cc_start: 0.8417 (m) cc_final: 0.7860 (t)
REVERT: S   80 PHE cc_start: 0.7753 (m-80) cc_final: 0.7279 (m-80)
REVERT: S  192 MET cc_start: 0.5493 (tpt) cc_final: 0.4733 (tpt)
REVERT: S  234 GLU cc_start: 0.6473 (OUTLIER) cc_final: 0.5997 (pp20)
REVERT: D   26 HIS cc_start: 0.5849 (OUTLIER) cc_final: 0.5274 (t70)
  outliers start: 21
  outliers final: 14
  residues processed: 262
  average time/residue: 0.1084
  time to fit residues: 38.0878
Evaluate side-chains
  272 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 251
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   69 MET
Chi-restraints excluded: chain R residue   31 ILE
Chi-restraints excluded: chain R residue  131 ILE
Chi-restraints excluded: chain R residue  181 CYS
Chi-restraints excluded: chain R residue  187 MET
Chi-restraints excluded: chain R residue  246 LEU
Chi-restraints excluded: chain R residue  250 ILE
Chi-restraints excluded: chain S residue   31 SER
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  174 LEU
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain S residue  233 LEU
Chi-restraints excluded: chain S residue  234 GLU
Chi-restraints excluded: chain D residue   26 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 32 optimal weight:    0.6980
   chunk 48 optimal weight:    0.3980
   chunk 104 optimal weight:    0.9980
   chunk 82 optimal weight:    0.7980
   chunk 54 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0050
   chunk 67 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 101 optimal weight:    0.0170
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.3832

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

Flipped N/Q/H residues before XYZ refinement:
R 301 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.189548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.162703 restraints weight = 13584.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.4015 rms_B_bonded: 2.89
r_work: 0.3882 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6712
moved from start:          0.2386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9289  Z= 0.133
  Angle     :  0.646   9.058  12586  Z= 0.338
  Chirality :  0.044   0.202   1421
  Planarity :  0.005   0.060   1590
  Dihedral  :  4.813  34.925   1261
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.48 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 20.16 %
    Favored  : 77.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.25), residues: 1142
  helix:  1.29 (0.27), residues: 378
  sheet:  0.02 (0.33), residues: 246
  loop : -2.02 (0.26), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 283 
 TYR   0.049   0.002   TYR R 114 
 PHE   0.026   0.001   PHE A 336 
 TRP   0.009   0.001   TRP B  63 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 9288)
  covalent geometry    : angle       0.64547 (12584)
  SS BOND              : bond        0.00033 (    1)
  SS BOND              : angle       2.15326 (    2)
  hydrogen bonds       : bond        0.03853 (  406)
  hydrogen bonds       : angle       4.69734 ( 1161)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2385.76 seconds
wall clock time: 41 minutes 40.02 seconds (2500.02 seconds total)