Starting phenix.real_space_refine
on Wed Feb  4 06:00:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kt9_62560/02_2026/9kt9_62560.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kt9_62560/02_2026/9kt9_62560.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kt9_62560/02_2026/9kt9_62560.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kt9_62560/02_2026/9kt9_62560.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kt9_62560/02_2026/9kt9_62560.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kt9_62560/02_2026/9kt9_62560.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      72      5.16       5
     C    5687      2.51       5
     N    1523      2.21       5
     O    1669      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8951
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1830
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1830
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 2, 'TRANS': 225}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2616
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
    Chain: "C"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "E"
      Number of atoms: 1791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1791
          Classifications: {'peptide': 233}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2267
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2267
          Classifications: {'peptide': 284}
          Link IDs: {'PTRANS': 13, 'TRANS': 270}
    Chain: "R"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 11
          Unusual residues: {'34D': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.12, per 1000 atoms: 0.24
  Number of scatterers: 8951
  At special positions: 0
  Unit cell: (90.206, 119.14, 130.203, 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      72     16.00
     O    1669      8.00
     N    1523      7.00
     C    5687      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R   6 " - pdb=" SG  CYS R 157 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R   7 " - pdb=" SG  CYS R 252 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  88 " - pdb=" SG  CYS R 165 " 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: 0.54
  Conformation dependent library (CDL) restraints added in 309.2 milliseconds
  

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2136

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 14 sheets defined
      33.3% alpha, 23.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.502A  pdb=" N   LYS A 210 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.633A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 231
      removed outlier: 4.528A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 271 through 281
      removed outlier: 3.738A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.914A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 352
    Processing helix  chain 'B' and resid 2 through 25
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'C' and resid 8 through 23
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 45 through 48
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'R' and resid 11 through 43
      removed outlier: 4.162A  pdb=" N   SER R  15 " --> pdb=" O   GLY R  11 " (cutoff:3.500A)
      Proline residue:  R  19  - end of helix
      removed outlier: 3.667A  pdb=" N   ALA R  30 " --> pdb=" O   PHE R  26 " (cutoff:3.500A)
      removed outlier: 5.145A  pdb=" N   LEU R  31 " --> pdb=" O   VAL R  27 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   GLY R  32 " --> pdb=" O   LEU R  28 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ASN R  33 " --> pdb=" O   GLY R  29 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   CYS R  41 " --> pdb=" O   LEU R  37 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 51 through 68
    Processing helix  chain 'R' and resid 69 through 72
    Processing helix  chain 'R' and resid 103 through 113
      removed outlier: 3.642A  pdb=" N   VAL R 109 " --> pdb=" O   PHE R 105 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 122 through 127
      removed outlier: 3.842A  pdb=" N   ILE R 127 " --> pdb=" O   VAL R 124 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 128 through 147
      removed outlier: 4.004A  pdb=" N   GLY R 134 " --> pdb=" O   ARG R 130 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   THR R 138 " --> pdb=" O   GLY R 134 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   TRP R 140 " --> pdb=" O   VAL R 136 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   ALA R 141 " --> pdb=" O   CYS R 137 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LEU R 142 " --> pdb=" O   THR R 138 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ILE R 144 " --> pdb=" O   TRP R 140 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   THR R 147 " --> pdb=" O   VAL R 143 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 178 through 205
      Proline residue:  R 188  - end of helix
      removed outlier: 3.516A  pdb=" N   ILE R 191 " --> pdb=" O   MET R 187 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ARG R 205 " --> pdb=" O   TRP R 201 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 212 through 246
      removed outlier: 3.600A  pdb=" N   LYS R 216 " --> pdb=" O   GLN R 212 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   MET R 223 " --> pdb=" O   THR R 219 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   VAL R 225 " --> pdb=" O   PHE R 221 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ALA R 226 " --> pdb=" O   ILE R 222 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   TYR R 233 " --> pdb=" O   PHE R 229 " (cutoff:3.500A)
      Proline residue:  R 235  - end of helix
      removed outlier: 3.513A  pdb=" N   ARG R 240 " --> pdb=" O   SER R 236 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 253 through 268
      removed outlier: 3.672A  pdb=" N   HIS R 261 " --> pdb=" O   HIS R 257 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ILE R 262 " --> pdb=" O   GLY R 258 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   SER R 265 " --> pdb=" O   HIS R 261 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 279
      Proline residue:  R 275  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.145A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.623A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.532A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.475A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.725A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.954A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.353A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.586A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.890A  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: 6.850A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.204A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.272A  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: 6.725A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.807A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.546A  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: 3.985A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 5.977A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.772A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 4.403A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141
      removed outlier: 3.599A  pdb=" N   ALA E 211 " --> pdb=" O   SER E 208 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
      removed outlier: 6.067A  pdb=" N   LEU E 178 " --> pdb=" O   LEU E 187 " (cutoff:3.500A)
      removed outlier: 5.417A  pdb=" N   LEU E 187 " --> pdb=" O   LEU E 178 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'R' and resid 156 through 158

    399 hydrogen bonds defined for protein.
    1092 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: 1.49

  Time building geometry restraints manager: 0.80 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2891
        1.35 -     1.46: 2270
        1.46 -     1.58: 3878
        1.58 -     1.70: 1
        1.70 -     1.82: 105
  Bond restraints: 9145
  Sorted by residual:
  bond pdb=" C3  34D R 401 "
       pdb=" O3  34D R 401 "
    ideal  model  delta    sigma   weight residual
    1.353  1.432 -0.079 2.00e-02 2.50e+03 1.57e+01
  bond pdb=" C5  34D R 401 "
       pdb=" O5  34D R 401 "
    ideal  model  delta    sigma   weight residual
    1.366  1.433 -0.067 2.00e-02 2.50e+03 1.14e+01
  bond pdb=" C   34D R 401 "
       pdb=" C1  34D R 401 "
    ideal  model  delta    sigma   weight residual
    1.529  1.594 -0.065 2.00e-02 2.50e+03 1.05e+01
  bond pdb=" C   34D R 401 "
       pdb=" O2  34D R 401 "
    ideal  model  delta    sigma   weight residual
    1.240  1.296 -0.056 2.00e-02 2.50e+03 7.94e+00
  bond pdb=" C   ILE R  86 "
       pdb=" N   PRO R  87 "
    ideal  model  delta    sigma   weight residual
    1.336  1.364 -0.028 1.08e-02 8.57e+03 6.91e+00
  ... (remaining 9140 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 12128
        1.76 -     3.51: 212
        3.51 -     5.27: 38
        5.27 -     7.03: 4
        7.03 -     8.79: 2
  Bond angle restraints: 12384
  Sorted by residual:
  angle pdb=" N   VAL R  90 "
        pdb=" CA  VAL R  90 "
        pdb=" C   VAL R  90 "
      ideal   model   delta    sigma   weight residual
     112.90  108.14    4.76 9.60e-01 1.09e+00 2.45e+01
  angle pdb=" N   VAL R 117 "
        pdb=" CA  VAL R 117 "
        pdb=" C   VAL R 117 "
      ideal   model   delta    sigma   weight residual
     113.71  109.29    4.42 9.50e-01 1.11e+00 2.17e+01
  angle pdb=" N   LEU R  95 "
        pdb=" CA  LEU R  95 "
        pdb=" C   LEU R  95 "
      ideal   model   delta    sigma   weight residual
     114.09  107.48    6.61 1.55e+00 4.16e-01 1.82e+01
  angle pdb=" N   ARG R  99 "
        pdb=" CA  ARG R  99 "
        pdb=" C   ARG R  99 "
      ideal   model   delta    sigma   weight residual
     113.97  108.99    4.98 1.28e+00 6.10e-01 1.51e+01
  angle pdb=" N   LEU R 106 "
        pdb=" CA  LEU R 106 "
        pdb=" C   LEU R 106 "
      ideal   model   delta    sigma   weight residual
     112.90  108.43    4.47 1.31e+00 5.83e-01 1.16e+01
  ... (remaining 12379 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.60: 4977
       17.60 -    35.20: 381
       35.20 -    52.80: 48
       52.80 -    70.39: 13
       70.39 -    87.99: 5
  Dihedral angle restraints: 5424
    sinusoidal: 2113
      harmonic: 3311
  Sorted by residual:
  dihedral pdb=" CB  CYS R   7 "
           pdb=" SG  CYS R   7 "
           pdb=" SG  CYS R 252 "
           pdb=" CB  CYS R 252 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  156.66  -63.66     1      1.00e+01 1.00e-02 5.34e+01
  dihedral pdb=" CB  CYS R   6 "
           pdb=" SG  CYS R   6 "
           pdb=" SG  CYS R 157 "
           pdb=" CB  CYS R 157 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -143.11   57.11     1      1.00e+01 1.00e-02 4.39e+01
  dihedral pdb=" CA  LEU A 268 "
           pdb=" C   LEU A 268 "
           pdb=" N   ASN A 269 "
           pdb=" CA  ASN A 269 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.47  -23.53     0      5.00e+00 4.00e-02 2.22e+01
  ... (remaining 5421 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 881
       0.034 -    0.067: 351
       0.067 -    0.101: 102
       0.101 -    0.134: 57
       0.134 -    0.168: 2
  Chirality restraints: 1393
  Sorted by residual:
  chirality pdb=" CA  GLU C  42 "
            pdb=" N   GLU C  42 "
            pdb=" C   GLU C  42 "
            pdb=" CB  GLU C  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.04e-01
  chirality pdb=" CG  LEU R  64 "
            pdb=" CB  LEU R  64 "
            pdb=" CD1 LEU R  64 "
            pdb=" CD2 LEU R  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.73    0.14 2.00e-01 2.50e+01 5.02e-01
  chirality pdb=" CA  ILE B 123 "
            pdb=" N   ILE B 123 "
            pdb=" C   ILE B 123 "
            pdb=" CB  ILE B 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.25e-01
  ... (remaining 1390 not shown)

  Planarity restraints: 1570
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO R  19 "    0.048 5.00e-02 4.00e+02   7.18e-02 8.25e+00
        pdb=" N   PRO R  20 "   -0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO R  20 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO R  20 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP R 274 "   -0.042 5.00e-02 4.00e+02   6.45e-02 6.65e+00
        pdb=" N   PRO R 275 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO R 275 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO R 275 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 247 "    0.042 5.00e-02 4.00e+02   6.40e-02 6.55e+00
        pdb=" N   PRO R 248 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO R 248 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO R 248 "    0.036 5.00e-02 4.00e+02
  ... (remaining 1567 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 2078
        2.79 -     3.32: 8111
        3.32 -     3.85: 14116
        3.85 -     4.37: 17139
        4.37 -     4.90: 29890
  Nonbonded interactions: 71334
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 247 "
            pdb=" OG1 THR B 249 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OG  SER R 236 "
            pdb=" OG1 THR R 267 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" O   TRP R  47 "
            pdb=" OG1 THR R 129 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" OE2 GLU A 318 "
            pdb=" OH  TYR A 320 "
     model   vdw
     2.346 3.040
  ... (remaining 71329 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.69 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     9.300
  Find NCS groups from input model:        0.050
  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:6.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
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   0.079   9149  Z= 0.139
  Angle     :  0.591   8.787  12392  Z= 0.337
  Chirality :  0.043   0.168   1393
  Planarity :  0.005   0.072   1570
  Dihedral  : 12.720  87.993   3276
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.33 (0.25), residues: 1128
  helix:  1.11 (0.30), residues: 354
  sheet:  1.08 (0.32), residues: 264
  loop : -0.89 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  32 
 TYR   0.010   0.001   TYR E 190 
 PHE   0.011   0.001   PHE B 234 
 TRP   0.012   0.001   TRP R 176 
 HIS   0.004   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 9145)
  covalent geometry    : angle       0.58968 (12384)
  SS BOND              : bond        0.00497 (    4)
  SS BOND              : angle       1.43767 (    8)
  hydrogen bonds       : bond        0.20225 (  392)
  hydrogen bonds       : angle       7.00820 ( 1092)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  323 ASP cc_start: 0.8061 (p0) cc_final: 0.7750 (p0)
REVERT: R   14 ILE cc_start: 0.5301 (mt) cc_final: 0.4829 (mt)
REVERT: R   26 PHE cc_start: 0.6040 (t80) cc_final: 0.5687 (t80)
REVERT: R   65 MET cc_start: 0.5507 (mmp) cc_final: 0.5124 (ptm)
REVERT: R   99 ARG cc_start: 0.6336 (tmt170) cc_final: 0.6094 (tmt170)
REVERT: R  130 ARG cc_start: 0.6126 (mtt90) cc_final: 0.5809 (mtp-110)
REVERT: R  145 LEU cc_start: 0.6578 (tt) cc_final: 0.5874 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 0.6164
  time to fit residues: 126.2385
Evaluate side-chains
  129 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:   20.0000
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0980
   chunk 100 optimal weight:   20.0000
   chunk 106 optimal weight:    6.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 269 ASN
A 294 ASN
B 259 GLN
R 125 ASN
R 257 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.166474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.104425 restraints weight = 10422.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 2.05
r_work: 0.3017 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2885 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2878
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2878 r_free = 0.2878    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2878 r_free = 0.2878    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2878
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9149  Z= 0.147
  Angle     :  0.610   8.034  12392  Z= 0.324
  Chirality :  0.045   0.159   1393
  Planarity :  0.005   0.057   1570
  Dihedral  :  4.869  23.733   1237
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 10.03 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.48 (0.25), residues: 1128
  helix:  1.36 (0.29), residues: 363
  sheet:  1.14 (0.31), residues: 279
  loop : -1.01 (0.26), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 134 
 TYR   0.015   0.001   TYR E 190 
 PHE   0.016   0.002   PHE R 243 
 TRP   0.010   0.002   TRP B  82 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 9145)
  covalent geometry    : angle       0.60883 (12384)
  SS BOND              : bond        0.00727 (    4)
  SS BOND              : angle       1.84078 (    8)
  hydrogen bonds       : bond        0.04516 (  392)
  hydrogen bonds       : angle       4.74157 ( 1092)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 142
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8590 (m-30) cc_final: 0.8370 (m-30)
REVERT: A   33 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7638 (mp0)
REVERT: A   47 ASN cc_start: 0.7439 (p0) cc_final: 0.7151 (m110)
REVERT: A  318 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7465 (pt0)
REVERT: E   11 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.8008 (mp)
REVERT: E  220 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7528 (mt-10)
REVERT: R   65 MET cc_start: 0.5792 (mmp) cc_final: 0.5044 (ptt)
REVERT: R   99 ARG cc_start: 0.6673 (tmt170) cc_final: 0.6407 (tmt170)
REVERT: R  130 ARG cc_start: 0.6347 (mtt90) cc_final: 0.5799 (mtp-110)
REVERT: R  180 MET cc_start: 0.5179 (ppp) cc_final: 0.4826 (pp-130)
REVERT: R  187 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6987 (ttm)
  outliers start: 32
  outliers final: 5
  residues processed: 157
  average time/residue: 0.6119
  time to fit residues: 101.3132
Evaluate side-chains
  130 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  156 SER
Chi-restraints excluded: chain R residue  183 LEU
Chi-restraints excluded: chain R residue  187 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 107 optimal weight:    4.9990
   chunk 106 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 99 optimal weight:    9.9990
   chunk 49 optimal weight:    0.5980
   overall best weight:    2.9188

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
B 259 GLN
R 155 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.163879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.101518 restraints weight = 10206.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 2.11
r_work: 0.2993 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2860 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2812
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2812 r_free = 0.2812    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2812 r_free = 0.2812    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2812
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.3539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9149  Z= 0.215
  Angle     :  0.686   9.655  12392  Z= 0.362
  Chirality :  0.048   0.159   1393
  Planarity :  0.005   0.054   1570
  Dihedral  :  5.318  27.025   1237
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 13.00 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.24 (0.25), residues: 1128
  helix:  1.13 (0.29), residues: 371
  sheet:  0.96 (0.30), residues: 284
  loop : -1.14 (0.25), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG R 205 
 TYR   0.012   0.002   TYR E  59 
 PHE   0.017   0.002   PHE B 151 
 TRP   0.012   0.002   TRP B  63 
 HIS   0.004   0.002   HIS R  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 ( 9145)
  covalent geometry    : angle       0.68510 (12384)
  SS BOND              : bond        0.01608 (    4)
  SS BOND              : angle       1.40668 (    8)
  hydrogen bonds       : bond        0.05463 (  392)
  hydrogen bonds       : angle       4.79499 ( 1092)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 132
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A   20 ASP cc_start: 0.8541 (m-30) cc_final: 0.8262 (m-30)
REVERT: A   25 GLU cc_start: 0.8198 (tt0) cc_final: 0.7601 (mt-10)
REVERT: A   33 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7435 (mp0)
REVERT: A  193 ASP cc_start: 0.7475 (m-30) cc_final: 0.7163 (t0)
REVERT: A  318 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7568 (pt0)
REVERT: A  349 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7938 (ttmt)
REVERT: B   44 GLN cc_start: 0.8076 (tp40) cc_final: 0.7555 (mt0)
REVERT: C   21 MET cc_start: 0.6399 (ttp) cc_final: 0.6120 (ttp)
REVERT: C   36 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7758 (m-30)
REVERT: E    7 SER cc_start: 0.8769 (m) cc_final: 0.8531 (p)
REVERT: E   11 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8256 (mp)
REVERT: E  218 ARG cc_start: 0.7748 (mtm110) cc_final: 0.7409 (tpp80)
REVERT: R  137 CYS cc_start: 0.6972 (m) cc_final: 0.5633 (p)
REVERT: R  170 MET cc_start: 0.4879 (OUTLIER) cc_final: 0.4559 (tpt)
REVERT: R  180 MET cc_start: 0.5231 (ppp) cc_final: 0.4926 (pp-130)
REVERT: R  187 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.6997 (ttm)
  outliers start: 37
  outliers final: 13
  residues processed: 148
  average time/residue: 0.5856
  time to fit residues: 91.2909
Evaluate side-chains
  138 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  349 LYS
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   43 LYS
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  156 SER
Chi-restraints excluded: chain R residue   66 ILE
Chi-restraints excluded: chain R residue  170 MET
Chi-restraints excluded: chain R residue  187 MET
Chi-restraints excluded: chain R residue  215 MET
Chi-restraints excluded: chain R residue  269 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 100 optimal weight:    2.9990
   chunk 64 optimal weight:    0.6980
   chunk 71 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9990
   chunk 18 optimal weight:    6.9990
   chunk 83 optimal weight:    0.8980
   chunk 94 optimal weight:    0.8980
   chunk 57 optimal weight:    9.9990
   chunk 53 optimal weight:    6.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A 294 ASN
B 340 ASN
C  59 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.167650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.111387 restraints weight = 10391.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 2.07
r_work: 0.3076 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2948 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2930
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2930 r_free = 0.2930    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2930 r_free = 0.2930    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2930
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.3626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   9149  Z= 0.110
  Angle     :  0.552   8.352  12392  Z= 0.288
  Chirality :  0.043   0.138   1393
  Planarity :  0.004   0.053   1570
  Dihedral  :  4.665  24.100   1237
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 15.66 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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: 1128
  helix:  1.60 (0.29), residues: 362
  sheet:  1.25 (0.31), residues: 276
  loop : -1.03 (0.25), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 134 
 TYR   0.014   0.001   TYR E 190 
 PHE   0.012   0.001   PHE A 189 
 TRP   0.012   0.001   TRP R 201 
 HIS   0.003   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 9145)
  covalent geometry    : angle       0.55159 (12384)
  SS BOND              : bond        0.00942 (    4)
  SS BOND              : angle       1.03001 (    8)
  hydrogen bonds       : bond        0.03582 (  392)
  hydrogen bonds       : angle       4.27760 ( 1092)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 132
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A   33 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7297 (mp0)
REVERT: A  193 ASP cc_start: 0.7433 (m-30) cc_final: 0.7131 (t0)
REVERT: A  318 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7458 (pt0)
REVERT: B   44 GLN cc_start: 0.8003 (tp40) cc_final: 0.7517 (mt0)
REVERT: B   45 MET cc_start: 0.9175 (mtt) cc_final: 0.8929 (mtt)
REVERT: B  228 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8307 (m-30)
REVERT: C   21 MET cc_start: 0.6447 (ttp) cc_final: 0.6034 (ttm)
REVERT: C   36 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7619 (m-30)
REVERT: E    7 SER cc_start: 0.8718 (m) cc_final: 0.8511 (p)
REVERT: R   65 MET cc_start: 0.6356 (mmp) cc_final: 0.5481 (ptt)
REVERT: R   99 ARG cc_start: 0.6540 (tmt170) cc_final: 0.6290 (tmt170)
REVERT: R  130 ARG cc_start: 0.6534 (mtt90) cc_final: 0.6085 (mtp-110)
REVERT: R  137 CYS cc_start: 0.6886 (m) cc_final: 0.5688 (p)
REVERT: R  170 MET cc_start: 0.4592 (OUTLIER) cc_final: 0.4346 (tpt)
REVERT: R  180 MET cc_start: 0.5458 (ppp) cc_final: 0.5101 (pp-130)
REVERT: R  187 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6894 (ttm)
  outliers start: 28
  outliers final: 8
  residues processed: 145
  average time/residue: 0.6746
  time to fit residues: 103.2831
Evaluate side-chains
  135 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  159 CYS
Chi-restraints excluded: chain R residue   92 LEU
Chi-restraints excluded: chain R residue  170 MET
Chi-restraints excluded: chain R residue  183 LEU
Chi-restraints excluded: chain R residue  187 MET
Chi-restraints excluded: chain R residue  215 MET
Chi-restraints excluded: chain R residue  269 MET
Chi-restraints excluded: chain R residue  272 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 73 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   chunk 103 optimal weight:    7.9990
   chunk 102 optimal weight:    0.9980
   chunk 48 optimal weight:    6.9990
   chunk 51 optimal weight:    5.9990
   chunk 17 optimal weight:    6.9990
   chunk 98 optimal weight:    6.9990
   chunk 110 optimal weight:    9.9990
   chunk 38 optimal weight:    8.9990
   chunk 109 optimal weight:    8.9990
   overall best weight:    3.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
A 306 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.161892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.102719 restraints weight = 10311.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 2.11
r_work: 0.2974 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2844 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2830
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2830 r_free = 0.2830    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2830 r_free = 0.2830    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2830
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.3926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   9149  Z= 0.248
  Angle     :  0.714  14.873  12392  Z= 0.371
  Chirality :  0.049   0.149   1393
  Planarity :  0.005   0.060   1570
  Dihedral  :  5.292  27.222   1237
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 15.86 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.24 (0.25), residues: 1128
  helix:  1.22 (0.29), residues: 370
  sheet:  0.92 (0.30), residues: 284
  loop : -1.19 (0.25), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R 205 
 TYR   0.013   0.002   TYR E 103 
 PHE   0.020   0.002   PHE B 151 
 TRP   0.013   0.002   TRP R 201 
 HIS   0.005   0.002   HIS R  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00591 ( 9145)
  covalent geometry    : angle       0.71385 (12384)
  SS BOND              : bond        0.01322 (    4)
  SS BOND              : angle       1.09329 (    8)
  hydrogen bonds       : bond        0.05483 (  392)
  hydrogen bonds       : angle       4.70660 ( 1092)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 122
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A   25 GLU cc_start: 0.8267 (tt0) cc_final: 0.7694 (mt-10)
REVERT: A   32 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7660 (mtp180)
REVERT: A   33 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7504 (mp0)
REVERT: A  193 ASP cc_start: 0.7483 (m-30) cc_final: 0.7185 (t0)
REVERT: A  232 LEU cc_start: 0.7498 (mt) cc_final: 0.7228 (mt)
REVERT: A  318 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7590 (pt0)
REVERT: B   44 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7550 (mt0)
REVERT: B  228 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.8502 (m-30)
REVERT: C   21 MET cc_start: 0.6389 (ttp) cc_final: 0.6075 (ttp)
REVERT: C   36 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7837 (m-30)
REVERT: E    7 SER cc_start: 0.8779 (m) cc_final: 0.8577 (p)
REVERT: R   65 MET cc_start: 0.6386 (mmp) cc_final: 0.5462 (ptt)
REVERT: R  130 ARG cc_start: 0.6731 (mtt90) cc_final: 0.6281 (mtp-110)
REVERT: R  137 CYS cc_start: 0.6989 (m) cc_final: 0.5776 (p)
REVERT: R  170 MET cc_start: 0.4572 (OUTLIER) cc_final: 0.4345 (tpt)
REVERT: R  180 MET cc_start: 0.5352 (ppp) cc_final: 0.5059 (pp-130)
REVERT: R  187 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6999 (ttm)
  outliers start: 44
  outliers final: 14
  residues processed: 147
  average time/residue: 0.6784
  time to fit residues: 105.3735
Evaluate side-chains
  134 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ARG
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  159 CYS
Chi-restraints excluded: chain R residue   37 LEU
Chi-restraints excluded: chain R residue   66 ILE
Chi-restraints excluded: chain R residue  170 MET
Chi-restraints excluded: chain R residue  183 LEU
Chi-restraints excluded: chain R residue  187 MET
Chi-restraints excluded: chain R residue  215 MET
Chi-restraints excluded: chain R residue  269 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 28 optimal weight:    0.8980
   chunk 87 optimal weight:    2.9990
   chunk 78 optimal weight:    0.0030
   chunk 9 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 97 optimal weight:   10.0000
   chunk 96 optimal weight:    0.8980
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.9594

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
** R  98 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 = 0.3982 r_free = 0.3982 target = 0.166282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.106246 restraints weight = 10407.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 1.99
r_work: 0.3048 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2897
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2897
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.3941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9149  Z= 0.113
  Angle     :  0.573  12.161  12392  Z= 0.297
  Chirality :  0.043   0.167   1393
  Planarity :  0.004   0.055   1570
  Dihedral  :  4.697  23.821   1237
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 18.01 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.59 (0.25), residues: 1128
  helix:  1.63 (0.29), residues: 368
  sheet:  1.17 (0.30), residues: 276
  loop : -1.09 (0.26), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 205 
 TYR   0.014   0.001   TYR E 190 
 PHE   0.013   0.001   PHE B 151 
 TRP   0.013   0.001   TRP R 201 
 HIS   0.004   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 9145)
  covalent geometry    : angle       0.57308 (12384)
  SS BOND              : bond        0.00720 (    4)
  SS BOND              : angle       0.66730 (    8)
  hydrogen bonds       : bond        0.03683 (  392)
  hydrogen bonds       : angle       4.23102 ( 1092)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 121
  time to evaluate  : 0.379 
Fit side-chains
REVERT: A   25 GLU cc_start: 0.8192 (tt0) cc_final: 0.7570 (mt-10)
REVERT: A   33 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7309 (mp0)
REVERT: A  193 ASP cc_start: 0.7497 (m-30) cc_final: 0.7186 (t0)
REVERT: A  229 ASP cc_start: 0.7726 (p0) cc_final: 0.7520 (m-30)
REVERT: A  318 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7525 (pt0)
REVERT: B   44 GLN cc_start: 0.8022 (tp40) cc_final: 0.7533 (mt0)
REVERT: C   21 MET cc_start: 0.6357 (ttp) cc_final: 0.5958 (ttm)
REVERT: C   36 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7685 (m-30)
REVERT: E   11 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8306 (mt)
REVERT: R   65 MET cc_start: 0.6345 (mmp) cc_final: 0.5414 (ptt)
REVERT: R  130 ARG cc_start: 0.6640 (mtt90) cc_final: 0.6164 (mtp-110)
REVERT: R  137 CYS cc_start: 0.6818 (m) cc_final: 0.5750 (p)
REVERT: R  170 MET cc_start: 0.4532 (OUTLIER) cc_final: 0.4324 (tpt)
REVERT: R  180 MET cc_start: 0.5339 (ppp) cc_final: 0.4985 (pp-130)
REVERT: R  187 MET cc_start: 0.7211 (tmm) cc_final: 0.6961 (ttm)
  outliers start: 25
  outliers final: 7
  residues processed: 134
  average time/residue: 0.6929
  time to fit residues: 98.2965
Evaluate side-chains
  125 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  159 CYS
Chi-restraints excluded: chain R residue   37 LEU
Chi-restraints excluded: chain R residue   66 ILE
Chi-restraints excluded: chain R residue  170 MET
Chi-restraints excluded: chain R residue  269 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 80 optimal weight:    7.9990
   chunk 63 optimal weight:    0.7980
   chunk 83 optimal weight:    0.2980
   chunk 58 optimal weight:    4.9990
   chunk 64 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 111 optimal weight:    2.9990
   chunk 109 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 104 optimal weight:    9.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
B 266 HIS
** R  98 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 = 0.3972 r_free = 0.3972 target = 0.165278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.104367 restraints weight = 10368.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 1.82
r_work: 0.3052 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2925 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2915
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2915
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8594
moved from start:          0.3995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9149  Z= 0.131
  Angle     :  0.588  10.406  12392  Z= 0.304
  Chirality :  0.044   0.139   1393
  Planarity :  0.004   0.054   1570
  Dihedral  :  4.700  23.835   1237
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 18.42 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.57 (0.25), residues: 1128
  helix:  1.69 (0.29), residues: 368
  sheet:  1.03 (0.30), residues: 276
  loop : -1.08 (0.26), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 205 
 TYR   0.013   0.001   TYR E 190 
 PHE   0.014   0.001   PHE B 199 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 9145)
  covalent geometry    : angle       0.58740 (12384)
  SS BOND              : bond        0.00865 (    4)
  SS BOND              : angle       0.75829 (    8)
  hydrogen bonds       : bond        0.03963 (  392)
  hydrogen bonds       : angle       4.24772 ( 1092)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 119
  time to evaluate  : 0.381 
Fit side-chains
REVERT: A   33 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7343 (mp0)
REVERT: A  193 ASP cc_start: 0.7441 (m-30) cc_final: 0.7185 (t0)
REVERT: A  318 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7505 (pt0)
REVERT: B   44 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7559 (mt0)
REVERT: C   21 MET cc_start: 0.6366 (ttp) cc_final: 0.5984 (ttm)
REVERT: C   36 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7719 (m-30)
REVERT: C   58 GLU cc_start: 0.7615 (pm20) cc_final: 0.7376 (pm20)
REVERT: E   11 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8282 (mt)
REVERT: R   65 MET cc_start: 0.6380 (mmp) cc_final: 0.5444 (ptt)
REVERT: R  130 ARG cc_start: 0.6671 (mtt90) cc_final: 0.6237 (mtp-110)
REVERT: R  137 CYS cc_start: 0.6829 (m) cc_final: 0.5800 (p)
REVERT: R  180 MET cc_start: 0.5481 (ppp) cc_final: 0.5126 (pp-130)
REVERT: R  187 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6910 (ttm)
  outliers start: 30
  outliers final: 13
  residues processed: 137
  average time/residue: 0.6980
  time to fit residues: 101.0542
Evaluate side-chains
  136 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  159 CYS
Chi-restraints excluded: chain R residue   37 LEU
Chi-restraints excluded: chain R residue   67 CYS
Chi-restraints excluded: chain R residue  183 LEU
Chi-restraints excluded: chain R residue  187 MET
Chi-restraints excluded: chain R residue  269 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 89 optimal weight:    0.9980
   chunk 78 optimal weight:    6.9990
   chunk 54 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 110 optimal weight:    7.9990
   chunk 99 optimal weight:    5.9990
   chunk 103 optimal weight:    7.9990
   chunk 104 optimal weight:    5.9990
   chunk 16 optimal weight:    0.8980
   overall best weight:    1.5382

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
** R  98 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 = 0.3970 r_free = 0.3970 target = 0.165047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.103773 restraints weight = 10313.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3179 rms_B_bonded: 1.84
r_work: 0.3038 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2911 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2916
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2916 r_free = 0.2916    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2916 r_free = 0.2916    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2916
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8585
moved from start:          0.4046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9149  Z= 0.138
  Angle     :  0.606   9.585  12392  Z= 0.314
  Chirality :  0.044   0.140   1393
  Planarity :  0.004   0.053   1570
  Dihedral  :  4.720  23.991   1237
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 19.04 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.59 (0.25), residues: 1128
  helix:  1.71 (0.29), residues: 368
  sheet:  1.01 (0.30), residues: 276
  loop : -1.06 (0.26), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 205 
 TYR   0.013   0.001   TYR E 190 
 PHE   0.015   0.002   PHE B 199 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 9145)
  covalent geometry    : angle       0.60581 (12384)
  SS BOND              : bond        0.00897 (    4)
  SS BOND              : angle       0.78701 (    8)
  hydrogen bonds       : bond        0.04022 (  392)
  hydrogen bonds       : angle       4.25489 ( 1092)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 118
  time to evaluate  : 0.375 
Fit side-chains
REVERT: A   33 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7350 (mp0)
REVERT: A  193 ASP cc_start: 0.7416 (m-30) cc_final: 0.7153 (t0)
REVERT: A  318 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7537 (pt0)
REVERT: B   44 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7524 (mt0)
REVERT: C   21 MET cc_start: 0.6357 (ttp) cc_final: 0.5973 (ttm)
REVERT: C   36 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7700 (m-30)
REVERT: C   58 GLU cc_start: 0.7561 (pm20) cc_final: 0.7330 (pm20)
REVERT: E   11 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8270 (mt)
REVERT: R   65 MET cc_start: 0.6384 (mmp) cc_final: 0.5352 (mtt)
REVERT: R  130 ARG cc_start: 0.6711 (mtt90) cc_final: 0.6254 (mtp-110)
REVERT: R  137 CYS cc_start: 0.6959 (m) cc_final: 0.5985 (p)
REVERT: R  170 MET cc_start: 0.4918 (tpt) cc_final: 0.4625 (tpt)
REVERT: R  180 MET cc_start: 0.5463 (ppp) cc_final: 0.5117 (pp-130)
REVERT: R  187 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6903 (ttm)
  outliers start: 28
  outliers final: 17
  residues processed: 137
  average time/residue: 0.7019
  time to fit residues: 101.7491
Evaluate side-chains
  138 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  159 CYS
Chi-restraints excluded: chain R residue   37 LEU
Chi-restraints excluded: chain R residue   67 CYS
Chi-restraints excluded: chain R residue  124 VAL
Chi-restraints excluded: chain R residue  183 LEU
Chi-restraints excluded: chain R residue  187 MET
Chi-restraints excluded: chain R residue  269 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0030
   chunk 98 optimal weight:    5.9990
   chunk 31 optimal weight:    0.8980
   chunk 24 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 88 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   chunk 86 optimal weight:   20.0000
   chunk 43 optimal weight:    3.9990
   chunk 71 optimal weight:    0.0770
   overall best weight:    0.9952

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
** R  98 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 = 0.3984 r_free = 0.3984 target = 0.166364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.105352 restraints weight = 10365.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 1.85
r_work: 0.3068 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2938 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2934
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2934 r_free = 0.2934    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2934 r_free = 0.2934    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2934
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.4085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9149  Z= 0.115
  Angle     :  0.576   9.015  12392  Z= 0.297
  Chirality :  0.043   0.151   1393
  Planarity :  0.004   0.054   1570
  Dihedral  :  4.549  22.855   1237
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 19.24 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.74 (0.25), residues: 1128
  helix:  1.83 (0.29), residues: 368
  sheet:  1.20 (0.30), residues: 272
  loop : -1.02 (0.26), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  62 
 TYR   0.014   0.001   TYR E 190 
 PHE   0.014   0.001   PHE R  83 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 9145)
  covalent geometry    : angle       0.57623 (12384)
  SS BOND              : bond        0.00714 (    4)
  SS BOND              : angle       0.71293 (    8)
  hydrogen bonds       : bond        0.03608 (  392)
  hydrogen bonds       : angle       4.12201 ( 1092)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 124
  time to evaluate  : 0.359 
Fit side-chains
REVERT: A   33 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7310 (mp0)
REVERT: A  193 ASP cc_start: 0.7419 (m-30) cc_final: 0.7164 (t0)
REVERT: A  318 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7498 (pt0)
REVERT: B   44 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7512 (mt0)
REVERT: C   21 MET cc_start: 0.6322 (ttp) cc_final: 0.5936 (ttm)
REVERT: C   36 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7715 (m-30)
REVERT: E   11 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8268 (mt)
REVERT: R   62 PHE cc_start: 0.7068 (t80) cc_final: 0.6462 (t80)
REVERT: R   65 MET cc_start: 0.6297 (mmp) cc_final: 0.5311 (mtt)
REVERT: R  130 ARG cc_start: 0.6672 (mtt90) cc_final: 0.6264 (mtp-110)
REVERT: R  137 CYS cc_start: 0.6930 (m) cc_final: 0.6008 (p)
REVERT: R  170 MET cc_start: 0.4741 (tpt) cc_final: 0.4467 (tpt)
REVERT: R  180 MET cc_start: 0.5548 (ppp) cc_final: 0.5205 (pp-130)
REVERT: R  187 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.6921 (ttm)
  outliers start: 26
  outliers final: 15
  residues processed: 141
  average time/residue: 0.6910
  time to fit residues: 103.2500
Evaluate side-chains
  141 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  159 CYS
Chi-restraints excluded: chain R residue    6 CYS
Chi-restraints excluded: chain R residue   37 LEU
Chi-restraints excluded: chain R residue   67 CYS
Chi-restraints excluded: chain R residue  183 LEU
Chi-restraints excluded: chain R residue  187 MET
Chi-restraints excluded: chain R residue  269 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 32 optimal weight:    3.9990
   chunk 53 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 22 optimal weight:    8.9990
   chunk 26 optimal weight:    7.9990
   chunk 67 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
** R  98 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 = 0.3981 r_free = 0.3981 target = 0.166115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.105607 restraints weight = 10312.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3215 rms_B_bonded: 1.81
r_work: 0.3070 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2933
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2933 r_free = 0.2933    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2933 r_free = 0.2933    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2933
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8575
moved from start:          0.4112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9149  Z= 0.118
  Angle     :  0.588   8.803  12392  Z= 0.303
  Chirality :  0.043   0.148   1393
  Planarity :  0.004   0.054   1570
  Dihedral  :  4.538  22.651   1237
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 19.65 %
    Favored  : 77.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.25), residues: 1128
  helix:  1.87 (0.29), residues: 368
  sheet:  1.18 (0.30), residues: 272
  loop : -1.00 (0.26), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  62 
 TYR   0.014   0.001   TYR E 190 
 PHE   0.013   0.001   PHE B 151 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 9145)
  covalent geometry    : angle       0.58817 (12384)
  SS BOND              : bond        0.00731 (    4)
  SS BOND              : angle       0.68844 (    8)
  hydrogen bonds       : bond        0.03615 (  392)
  hydrogen bonds       : angle       4.10641 ( 1092)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 0.389 
Fit side-chains
REVERT: A   33 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7306 (mp0)
REVERT: A  193 ASP cc_start: 0.7433 (m-30) cc_final: 0.7174 (t0)
REVERT: A  318 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7488 (pt0)
REVERT: B   44 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7504 (mt0)
REVERT: C   21 MET cc_start: 0.6372 (ttp) cc_final: 0.6011 (ttm)
REVERT: C   36 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7716 (m-30)
REVERT: E   11 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8277 (mt)
REVERT: R   62 PHE cc_start: 0.7115 (t80) cc_final: 0.6532 (t80)
REVERT: R   65 MET cc_start: 0.6283 (mmp) cc_final: 0.5325 (mtt)
REVERT: R  130 ARG cc_start: 0.6661 (mtt90) cc_final: 0.6267 (mtp-110)
REVERT: R  180 MET cc_start: 0.5586 (ppp) cc_final: 0.5244 (pp-130)
REVERT: R  187 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6910 (ttm)
  outliers start: 24
  outliers final: 15
  residues processed: 138
  average time/residue: 0.6431
  time to fit residues: 93.9607
Evaluate side-chains
  139 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  159 CYS
Chi-restraints excluded: chain R residue    6 CYS
Chi-restraints excluded: chain R residue   37 LEU
Chi-restraints excluded: chain R residue  183 LEU
Chi-restraints excluded: chain R residue  187 MET
Chi-restraints excluded: chain R residue  269 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0170
   chunk 39 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 104 optimal weight:    0.0570
   chunk 63 optimal weight:    7.9990
   chunk 101 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.5736

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.168207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.108755 restraints weight = 10253.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 1.88
r_work: 0.3096 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2957
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2957
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.4149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   9149  Z= 0.103
  Angle     :  0.576  12.776  12392  Z= 0.294
  Chirality :  0.043   0.158   1393
  Planarity :  0.004   0.053   1570
  Dihedral  :  4.349  21.251   1237
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 20.16 %
    Favored  : 77.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.91 (0.25), residues: 1128
  helix:  2.09 (0.29), residues: 362
  sheet:  1.31 (0.31), residues: 258
  loop : -0.93 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  62 
 TYR   0.015   0.001   TYR E 190 
 PHE   0.012   0.001   PHE R  83 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 9145)
  covalent geometry    : angle       0.57610 (12384)
  SS BOND              : bond        0.00577 (    4)
  SS BOND              : angle       0.63164 (    8)
  hydrogen bonds       : bond        0.03186 (  392)
  hydrogen bonds       : angle       3.97162 ( 1092)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4482.04 seconds
wall clock time: 76 minutes 59.31 seconds (4619.31 seconds total)