Starting phenix.real_space_refine
on Fri Oct 10 20:41:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wwm_37893/10_2025/8wwm_37893.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wwm_37893/10_2025/8wwm_37893.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wwm_37893/10_2025/8wwm_37893.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wwm_37893/10_2025/8wwm_37893.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wwm_37893/10_2025/8wwm_37893.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wwm_37893/10_2025/8wwm_37893.map"
  }
  resolution = 2.81
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.063
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      68      5.16       5
     C    5708      2.51       5
     N    1517      2.21       5
     O    1670      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8963
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1749
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 2, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 32
    Chain: "B"
      Number of atoms: 2622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 342, 2622
          Classifications: {'peptide': 342}
          Link IDs: {'PTRANS': 5, 'TRANS': 336}
    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: 1779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1779
          Classifications: {'peptide': 231}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2238
          Classifications: {'peptide': 289}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 15, 'TRANS': 273}
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 65
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 32
    Chain: "L"
      Number of atoms: 139
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 139
          Classifications: {'peptide': 17}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 15}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 9
  Time building chain proxies: 2.09, per 1000 atoms: 0.23
  Number of scatterers: 8963
  At special positions: 0
  Unit cell: (88.81, 115.56, 128.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      68     16.00
     O    1670      8.00
     N    1517      7.00
     C    5708      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 185 " - pdb=" SG  CYS R 263 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L   7 " - pdb=" SG  CYS L  16 " 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: 0.71
  Conformation dependent library (CDL) restraints added in 310.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2172

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 15 sheets defined
      38.0% alpha, 23.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.606A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 52
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 4.062A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.862A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.632A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.974A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 352
    Processing helix  chain 'B' and resid 3 through 25
      removed outlier: 3.524A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 7 through 24
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'R' and resid 108 through 136
      removed outlier: 3.893A  pdb=" N   MET R 112 " --> pdb=" O   ILE R 108 " (cutoff:3.500A)
      Proline residue:  R 113  - end of helix
    Processing helix  chain 'R' and resid 145 through 164
      removed outlier: 3.909A  pdb=" N   PHE R 150 " --> pdb=" O   VAL R 146 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ILE R 152 " --> pdb=" O   ASP R 148 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 165 through 174
      removed outlier: 6.177A  pdb=" N   GLN R 171 " --> pdb=" O   PHE R 167 " (cutoff:3.500A)
      removed outlier: 5.356A  pdb=" N   LEU R 172 " --> pdb=" O   MET R 168 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   MET R 173 " --> pdb=" O   ILE R 169 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   GLY R 174 " --> pdb=" O   HIS R 170 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 180 through 216
      removed outlier: 3.753A  pdb=" N   MET R 184 " --> pdb=" O   PHE R 180 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   THR R 186 " --> pdb=" O   GLU R 182 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   LEU R 187 " --> pdb=" O   THR R 183 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   SER R 199 " --> pdb=" O   SER R 195 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 218 through 223
      removed outlier: 3.538A  pdb=" N   THR R 221 " --> pdb=" O   ILE R 218 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 225 through 244
      removed outlier: 3.514A  pdb=" N   ALA R 238 " --> pdb=" O   CYS R 234 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 244 through 250
      removed outlier: 3.502A  pdb=" N   TRP R 248 " --> pdb=" O   ILE R 244 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 286
      removed outlier: 3.849A  pdb=" N   LEU R 274 " --> pdb=" O   PRO R 270 " (cutoff:3.500A)
      removed outlier: 5.935A  pdb=" N   TYR R 275 " --> pdb=" O   ASP R 271 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   TRP R 276 " --> pdb=" O   THR R 272 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   PHE R 277 " --> pdb=" O   ASP R 273 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 286 through 303
    Processing helix  chain 'R' and resid 313 through 348
      Proline residue:  R 340  - end of helix
      removed outlier: 3.753A  pdb=" N   GLN R 345 " --> pdb=" O   TYR R 341 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 355 through 384
      removed outlier: 4.226A  pdb=" N   SER R 373 " --> pdb=" O   GLY R 369 " (cutoff:3.500A)
      Proline residue:  R 377  - end of helix
    Processing helix  chain 'R' and resid 384 through 395
      removed outlier: 3.646A  pdb=" N   ARG R 388 " --> pdb=" O   CYS R 384 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LYS R 389 " --> pdb=" O   GLU R 385 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   SER R 394 " --> pdb=" O   ARG R 390 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   VAL R 395 " --> pdb=" O   LEU R 391 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.254A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.429A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.047A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.427A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.540A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.849A  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: 5.975A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.023A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.305A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.674A  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: 6.891A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.062A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.260A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.254A  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: 6.481A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.894A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.074A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.904A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.646A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.270A  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 11 through 12
      removed outlier: 6.743A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12
      removed outlier: 4.141A  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
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
      removed outlier: 3.573A  pdb=" N   ILE E 189 " --> pdb=" O   TRP E 176 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   LEU E 178 " --> pdb=" O   LEU E 187 " (cutoff:3.500A)
      removed outlier: 5.592A  pdb=" N   LEU E 187 " --> pdb=" O   LEU E 178 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'R' and resid 251 through 255
    Processing sheet with id=AB6, first strand: chain 'L' and resid 8 through 9
      removed outlier: 3.648A  pdb=" N   VAL L  12 " --> pdb=" O   LEU L   9 " (cutoff:3.500A)

    453 hydrogen bonds defined for protein.
    1263 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: 1.57

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2887
        1.34 -     1.46: 2082
        1.46 -     1.58: 4086
        1.58 -     1.70: 0
        1.70 -     1.81: 99
  Bond restraints: 9154
  Sorted by residual:
  bond pdb=" CG1 ILE B 273 "
       pdb=" CD1 ILE B 273 "
    ideal  model  delta    sigma   weight residual
    1.513  1.464  0.049 3.90e-02 6.57e+02 1.56e+00
  bond pdb=" CG1 ILE B  81 "
       pdb=" CD1 ILE B  81 "
    ideal  model  delta    sigma   weight residual
    1.513  1.474  0.039 3.90e-02 6.57e+02 1.00e+00
  bond pdb=" CG  LEU B 318 "
       pdb=" CD1 LEU B 318 "
    ideal  model  delta    sigma   weight residual
    1.521  1.489  0.032 3.30e-02 9.18e+02 9.45e-01
  bond pdb=" CB  TRP B 211 "
       pdb=" CG  TRP B 211 "
    ideal  model  delta    sigma   weight residual
    1.498  1.471  0.027 3.10e-02 1.04e+03 7.45e-01
  bond pdb=" CG  LEU B 318 "
       pdb=" CD2 LEU B 318 "
    ideal  model  delta    sigma   weight residual
    1.521  1.493  0.028 3.30e-02 9.18e+02 6.97e-01
  ... (remaining 9149 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.27: 12130
        1.27 -     2.55: 238
        2.55 -     3.82: 42
        3.82 -     5.09: 11
        5.09 -     6.37: 3
  Bond angle restraints: 12424
  Sorted by residual:
  angle pdb=" C   ARG E 191 "
        pdb=" N   MET E 192 "
        pdb=" CA  MET E 192 "
      ideal   model   delta    sigma   weight residual
     121.54  125.64   -4.10 1.91e+00 2.74e-01 4.62e+00
  angle pdb=" CA  LEU B 318 "
        pdb=" CB  LEU B 318 "
        pdb=" CG  LEU B 318 "
      ideal   model   delta    sigma   weight residual
     116.30  122.57   -6.27 3.50e+00 8.16e-02 3.21e+00
  angle pdb=" N   TYR E 102 "
        pdb=" CA  TYR E 102 "
        pdb=" C   TYR E 102 "
      ideal   model   delta    sigma   weight residual
     108.74  106.39    2.35 1.38e+00 5.25e-01 2.91e+00
  angle pdb=" CA  LEU B 190 "
        pdb=" CB  LEU B 190 "
        pdb=" CG  LEU B 190 "
      ideal   model   delta    sigma   weight residual
     116.30  121.92   -5.62 3.50e+00 8.16e-02 2.58e+00
  angle pdb=" C   TYR E 101 "
        pdb=" N   TYR E 102 "
        pdb=" CA  TYR E 102 "
      ideal   model   delta    sigma   weight residual
     122.11  124.43   -2.32 1.59e+00 3.96e-01 2.14e+00
  ... (remaining 12419 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.10: 5203
       17.10 -    34.20: 179
       34.20 -    51.30: 32
       51.30 -    68.40: 8
       68.40 -    85.49: 2
  Dihedral angle restraints: 5424
    sinusoidal: 2058
      harmonic: 3366
  Sorted by residual:
  dihedral pdb=" CA  GLN B  75 "
           pdb=" C   GLN B  75 "
           pdb=" N   ASP B  76 "
           pdb=" CA  ASP B  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.63   20.37     0      5.00e+00 4.00e-02 1.66e+01
  dihedral pdb=" CA  PHE E  32 "
           pdb=" C   PHE E  32 "
           pdb=" N   GLY E  33 "
           pdb=" CA  GLY E  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.96   19.04     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CA  HIS E  35 "
           pdb=" C   HIS E  35 "
           pdb=" N   TRP E  36 "
           pdb=" CA  TRP E  36 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.53   17.47     0      5.00e+00 4.00e-02 1.22e+01
  ... (remaining 5421 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 760
       0.028 -    0.055: 427
       0.055 -    0.083: 137
       0.083 -    0.110: 76
       0.110 -    0.138: 26
  Chirality restraints: 1426
  Sorted by residual:
  chirality pdb=" CA  SER B 334 "
            pdb=" N   SER B 334 "
            pdb=" C   SER B 334 "
            pdb=" CB  SER B 334 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.75e-01
  chirality pdb=" CA  THR B  87 "
            pdb=" N   THR B  87 "
            pdb=" C   THR B  87 "
            pdb=" CB  THR B  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.39    0.14 2.00e-01 2.50e+01 4.59e-01
  chirality pdb=" CA  ILE B 120 "
            pdb=" N   ILE B 120 "
            pdb=" C   ILE B 120 "
            pdb=" CB  ILE B 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.52e-01
  ... (remaining 1423 not shown)

  Planarity restraints: 1571
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.033 5.00e-02 4.00e+02   4.91e-02 3.85e+00
        pdb=" N   PRO B 236 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C  48 "    0.024 5.00e-02 4.00e+02   3.71e-02 2.20e+00
        pdb=" N   PRO C  49 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO C  49 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C  49 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B  71 "   -0.006 2.00e-02 2.50e+03   1.25e-02 1.57e+00
        pdb=" C   VAL B  71 "    0.022 2.00e-02 2.50e+03
        pdb=" O   VAL B  71 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   SER B  72 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1568 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1277
        2.75 -     3.29: 8560
        3.29 -     3.83: 15134
        3.83 -     4.36: 18994
        4.36 -     4.90: 32634
  Nonbonded interactions: 76599
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 320 "
            pdb=" OD2 ASP A 341 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" NE2 GLN R 196 "
            pdb=" OH  TYR R 342 "
     model   vdw
     2.220 3.120
  nonbonded pdb=" O   ILE R 149 "
            pdb=" ND2 ASN R 153 "
     model   vdw
     2.222 3.120
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.236 3.040
  ... (remaining 76594 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.430
  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:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.090
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  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:8.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9158  Z= 0.182
  Angle     :  0.482   6.368  12432  Z= 0.253
  Chirality :  0.042   0.138   1426
  Planarity :  0.004   0.049   1571
  Dihedral  :  9.438  85.494   3240
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  3.10 %
    Favored  : 95.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 aren not related in a simple way.
  whole:  0.54 (0.24), residues: 1144
  helix:  0.73 (0.26), residues: 393
  sheet:  0.62 (0.29), residues: 296
  loop :  0.01 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  14 
 TYR   0.011   0.002   TYR R 280 
 PHE   0.013   0.002   PHE B 199 
 TRP   0.013   0.002   TRP B 339 
 HIS   0.004   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 9154)
  covalent geometry    : angle       0.48152 (12424)
  SS BOND              : bond        0.00156 (    4)
  SS BOND              : angle       0.84672 (    8)
  hydrogen bonds       : bond        0.24891 (  448)
  hydrogen bonds       : angle       7.75003 ( 1263)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 209
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8293 (mttt) cc_final: 0.7900 (mmtm)
REVERT: A   21 ARG cc_start: 0.7927 (ttm170) cc_final: 0.7618 (mtm110)
REVERT: A   22 ASN cc_start: 0.8108 (m-40) cc_final: 0.7847 (m110)
REVERT: A   29 LYS cc_start: 0.8529 (tttt) cc_final: 0.7733 (mtmt)
REVERT: A  208 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.7690 (ttp80)
REVERT: A  275 GLU cc_start: 0.8055 (tt0) cc_final: 0.7772 (tm-30)
REVERT: A  306 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7539 (mm-40)
REVERT: A  349 LYS cc_start: 0.7671 (mttt) cc_final: 0.7300 (mtmt)
REVERT: B   42 ARG cc_start: 0.7286 (tpt170) cc_final: 0.7014 (tmt170)
REVERT: B   48 ARG cc_start: 0.8239 (mmt180) cc_final: 0.7859 (mmt180)
REVERT: B   52 ARG cc_start: 0.8385 (mtt-85) cc_final: 0.8151 (mtt90)
REVERT: B  129 ARG cc_start: 0.7944 (mtp180) cc_final: 0.7465 (ttt90)
REVERT: B  153 ASP cc_start: 0.8910 (p0) cc_final: 0.8664 (p0)
REVERT: B  226 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7470 (mm-30)
REVERT: B  293 ASN cc_start: 0.8344 (m-40) cc_final: 0.8043 (m-40)
REVERT: C   21 MET cc_start: 0.7538 (mmm) cc_final: 0.7326 (mtm)
REVERT: C   47 GLU cc_start: 0.7532 (pt0) cc_final: 0.7153 (pm20)
REVERT: E   21 SER cc_start: 0.8747 (m) cc_final: 0.8503 (t)
REVERT: E   63 THR cc_start: 0.8049 (t) cc_final: 0.7769 (p)
REVERT: E  186 GLN cc_start: 0.8346 (tt0) cc_final: 0.8029 (tt0)
REVERT: R  163 LEU cc_start: 0.6719 (mt) cc_final: 0.6496 (mt)
REVERT: R  322 ARG cc_start: 0.6325 (mtt180) cc_final: 0.6076 (mtm-85)
REVERT: R  345 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6960 (mp10)
  outliers start: 9
  outliers final: 5
  residues processed: 215
  average time/residue: 0.5305
  time to fit residues: 121.5518
Evaluate side-chains
  153 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 147
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain R residue  209 ASP
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  345 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    9.9990
   chunk 106 optimal weight:    5.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 GLN
B 176 GLN
E 179 GLN
E 183 GLN
E 194 ASN
R 194 ASN
R 281 GLN
R 345 GLN
R 348 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.191622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.133934 restraints weight = 9436.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 1.84
r_work: 0.3413 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3296 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          0.1788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9158  Z= 0.151
  Angle     :  0.574  11.296  12432  Z= 0.302
  Chirality :  0.044   0.160   1426
  Planarity :  0.004   0.048   1571
  Dihedral  :  5.552  73.373   1264
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 11.88 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 aren not related in a simple way.
  whole:  1.05 (0.25), residues: 1144
  helix:  1.77 (0.26), residues: 387
  sheet:  0.68 (0.30), residues: 286
  loop : -0.12 (0.28), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L  11 
 TYR   0.018   0.002   TYR R 275 
 PHE   0.013   0.001   PHE R 241 
 TRP   0.020   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 9154)
  covalent geometry    : angle       0.57385 (12424)
  SS BOND              : bond        0.00238 (    4)
  SS BOND              : angle       0.85849 (    8)
  hydrogen bonds       : bond        0.05245 (  448)
  hydrogen bonds       : angle       5.27780 ( 1263)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 151
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8015 (mttt) cc_final: 0.7352 (mmtm)
REVERT: A   18 MET cc_start: 0.8168 (mtp) cc_final: 0.7938 (mtp)
REVERT: A   21 ARG cc_start: 0.7358 (ttm170) cc_final: 0.7013 (mtm110)
REVERT: A   28 GLU cc_start: 0.6810 (mt-10) cc_final: 0.5918 (mm-30)
REVERT: A   29 LYS cc_start: 0.8307 (tttt) cc_final: 0.7591 (ttmt)
REVERT: A  208 ARG cc_start: 0.8109 (ttm-80) cc_final: 0.7267 (ttp80)
REVERT: A  275 GLU cc_start: 0.8115 (tt0) cc_final: 0.7721 (tm-30)
REVERT: A  330 LYS cc_start: 0.6641 (mttt) cc_final: 0.5569 (tttm)
REVERT: A  349 LYS cc_start: 0.7516 (mttt) cc_final: 0.7160 (mttt)
REVERT: B   42 ARG cc_start: 0.7267 (tpt170) cc_final: 0.6955 (tmt170)
REVERT: B   46 ARG cc_start: 0.7825 (mtp-110) cc_final: 0.7314 (mtm-85)
REVERT: B   52 ARG cc_start: 0.8601 (mtt-85) cc_final: 0.8162 (mtt90)
REVERT: B  129 ARG cc_start: 0.7988 (mtp180) cc_final: 0.7363 (ttt90)
REVERT: B  153 ASP cc_start: 0.8845 (p0) cc_final: 0.8618 (p0)
REVERT: B  217 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8239 (pmt)
REVERT: B  226 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7298 (mm-30)
REVERT: C   21 MET cc_start: 0.7577 (mmm) cc_final: 0.7094 (ttm)
REVERT: C   47 GLU cc_start: 0.7475 (pt0) cc_final: 0.6834 (pm20)
REVERT: E  186 GLN cc_start: 0.8404 (tt0) cc_final: 0.8073 (tm-30)
REVERT: R  112 MET cc_start: 0.3422 (mpp) cc_final: 0.2911 (mmt)
REVERT: R  163 LEU cc_start: 0.6661 (mt) cc_final: 0.6308 (mt)
REVERT: R  322 ARG cc_start: 0.6128 (mtt180) cc_final: 0.5910 (mtm-85)
REVERT: R  345 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6501 (mp10)
REVERT: R  391 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7262 (mt)
REVERT: L    8 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.7142 (tpp)
REVERT: L   14 ARG cc_start: 0.5870 (ptm-80) cc_final: 0.5507 (ppt170)
  outliers start: 36
  outliers final: 9
  residues processed: 169
  average time/residue: 0.5462
  time to fit residues: 97.9911
Evaluate side-chains
  156 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 143
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  162 SER
Chi-restraints excluded: chain R residue  209 ASP
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  345 GLN
Chi-restraints excluded: chain R residue  391 LEU
Chi-restraints excluded: chain L residue    8 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 85 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 107 optimal weight:    2.9990
   chunk 108 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 74 optimal weight:   10.0000
   chunk 46 optimal weight:    0.5980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 322 HIS
R 170 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.190009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.132419 restraints weight = 9444.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3508 rms_B_bonded: 1.83
r_work: 0.3407 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3290 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9158  Z= 0.183
  Angle     :  0.561   8.441  12432  Z= 0.298
  Chirality :  0.044   0.169   1426
  Planarity :  0.004   0.049   1571
  Dihedral  :  5.529  67.721   1262
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 13.02 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 aren not related in a simple way.
  whole:  0.87 (0.25), residues: 1144
  helix:  1.89 (0.27), residues: 384
  sheet:  0.23 (0.29), residues: 285
  loop : -0.21 (0.28), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R 299 
 TYR   0.012   0.002   TYR R 275 
 PHE   0.014   0.002   PHE R 150 
 TRP   0.019   0.002   TRP B 169 
 HIS   0.006   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 9154)
  covalent geometry    : angle       0.56067 (12424)
  SS BOND              : bond        0.00255 (    4)
  SS BOND              : angle       0.99743 (    8)
  hydrogen bonds       : bond        0.04825 (  448)
  hydrogen bonds       : angle       5.10725 ( 1263)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 144
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8013 (mttt) cc_final: 0.7393 (mmtm)
REVERT: A   18 MET cc_start: 0.8141 (mtp) cc_final: 0.7913 (mtp)
REVERT: A   21 ARG cc_start: 0.7344 (ttm170) cc_final: 0.7106 (mtm-85)
REVERT: A   28 GLU cc_start: 0.6818 (mt-10) cc_final: 0.5913 (mm-30)
REVERT: A   29 LYS cc_start: 0.8317 (tttt) cc_final: 0.7202 (mtmt)
REVERT: A  186 GLU cc_start: 0.8343 (tt0) cc_final: 0.7587 (mt-10)
REVERT: A  208 ARG cc_start: 0.7945 (ttm-80) cc_final: 0.7202 (ttp80)
REVERT: A  275 GLU cc_start: 0.7984 (tt0) cc_final: 0.7733 (tm-30)
REVERT: A  330 LYS cc_start: 0.6648 (mttt) cc_final: 0.5587 (tttm)
REVERT: A  349 LYS cc_start: 0.7529 (mttt) cc_final: 0.7141 (mttt)
REVERT: B   42 ARG cc_start: 0.7122 (tpt170) cc_final: 0.6689 (tmt170)
REVERT: B   46 ARG cc_start: 0.8007 (mtp-110) cc_final: 0.7520 (mtm-85)
REVERT: B   52 ARG cc_start: 0.8631 (mtt-85) cc_final: 0.8224 (mtt90)
REVERT: B   61 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8466 (ppp)
REVERT: B  129 ARG cc_start: 0.8059 (mtp180) cc_final: 0.7401 (ttt90)
REVERT: B  153 ASP cc_start: 0.8824 (p0) cc_final: 0.8587 (p0)
REVERT: B  217 MET cc_start: 0.8521 (pmm) cc_final: 0.8289 (pmt)
REVERT: B  226 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7292 (mm-30)
REVERT: C   21 MET cc_start: 0.7510 (mmm) cc_final: 0.7072 (ttm)
REVERT: C   47 GLU cc_start: 0.7498 (pt0) cc_final: 0.6931 (pm20)
REVERT: E  186 GLN cc_start: 0.8382 (tt0) cc_final: 0.8056 (tm-30)
REVERT: R  163 LEU cc_start: 0.6586 (mt) cc_final: 0.6225 (mt)
REVERT: R  165 MET cc_start: 0.5636 (ttt) cc_final: 0.5157 (tpt)
REVERT: R  322 ARG cc_start: 0.6098 (mtt180) cc_final: 0.5876 (mtm-85)
REVERT: R  345 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6693 (mp10)
REVERT: R  391 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7257 (mt)
REVERT: L    8 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7191 (tpp)
REVERT: L   14 ARG cc_start: 0.5922 (ptm-80) cc_final: 0.5375 (ppt170)
  outliers start: 35
  outliers final: 15
  residues processed: 158
  average time/residue: 0.6115
  time to fit residues: 102.2745
Evaluate side-chains
  158 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  162 SER
Chi-restraints excluded: chain E residue  166 LEU
Chi-restraints excluded: chain R residue  209 ASP
Chi-restraints excluded: chain R residue  267 LEU
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  345 GLN
Chi-restraints excluded: chain R residue  391 LEU
Chi-restraints excluded: chain R residue  393 LEU
Chi-restraints excluded: chain L residue    8 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 53 optimal weight:    0.0010
   chunk 112 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 98 optimal weight:    0.0470
   chunk 64 optimal weight:    0.8980
   chunk 96 optimal weight:    4.9990
   chunk 28 optimal weight:    0.4980
   chunk 31 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 106 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.4084

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN
R 345 GLN
R 348 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.191611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.133522 restraints weight = 9588.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 1.90
r_work: 0.3446 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3329 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9158  Z= 0.113
  Angle     :  0.507   8.566  12432  Z= 0.266
  Chirality :  0.042   0.208   1426
  Planarity :  0.003   0.049   1571
  Dihedral  :  5.069  54.418   1262
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 14.98 %
    Favored  : 82.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 aren not related in a simple way.
  whole:  0.99 (0.25), residues: 1144
  helix:  2.09 (0.27), residues: 384
  sheet:  0.22 (0.29), residues: 282
  loop : -0.19 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R 303 
 TYR   0.012   0.001   TYR E 190 
 PHE   0.010   0.001   PHE B 199 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 9154)
  covalent geometry    : angle       0.50732 (12424)
  SS BOND              : bond        0.00208 (    4)
  SS BOND              : angle       0.59469 (    8)
  hydrogen bonds       : bond        0.03991 (  448)
  hydrogen bonds       : angle       4.77605 ( 1263)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 156
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.7939 (mttt) cc_final: 0.7334 (mmtm)
REVERT: A   21 ARG cc_start: 0.7213 (ttm170) cc_final: 0.6945 (mtm110)
REVERT: A   22 ASN cc_start: 0.7635 (m-40) cc_final: 0.7369 (m110)
REVERT: A   28 GLU cc_start: 0.6770 (mt-10) cc_final: 0.5876 (mm-30)
REVERT: A   29 LYS cc_start: 0.8224 (tttt) cc_final: 0.7369 (ttmm)
REVERT: A  186 GLU cc_start: 0.8296 (tt0) cc_final: 0.7562 (mt-10)
REVERT: A  208 ARG cc_start: 0.7909 (ttm-80) cc_final: 0.7255 (ttp80)
REVERT: A  330 LYS cc_start: 0.6570 (mttt) cc_final: 0.5474 (tttm)
REVERT: A  349 LYS cc_start: 0.7496 (mttt) cc_final: 0.7154 (mttp)
REVERT: B   42 ARG cc_start: 0.7172 (tpt170) cc_final: 0.6736 (tmt170)
REVERT: B   46 ARG cc_start: 0.7987 (mtp-110) cc_final: 0.7502 (mtm-85)
REVERT: B   52 ARG cc_start: 0.8618 (mtt-85) cc_final: 0.8236 (mtt90)
REVERT: B  129 ARG cc_start: 0.8049 (mtp180) cc_final: 0.7357 (ttt90)
REVERT: B  153 ASP cc_start: 0.8912 (p0) cc_final: 0.8615 (p0)
REVERT: B  226 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7297 (mp0)
REVERT: B  241 PHE cc_start: 0.9025 (p90) cc_final: 0.8661 (p90)
REVERT: C   21 MET cc_start: 0.7467 (mmm) cc_final: 0.7010 (ttm)
REVERT: C   37 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7137 (tp)
REVERT: C   47 GLU cc_start: 0.7385 (pt0) cc_final: 0.6746 (pm20)
REVERT: E  186 GLN cc_start: 0.8450 (tt0) cc_final: 0.8112 (tm-30)
REVERT: R  163 LEU cc_start: 0.6598 (mt) cc_final: 0.6264 (mt)
REVERT: R  165 MET cc_start: 0.5506 (ttt) cc_final: 0.5149 (tpt)
REVERT: R  208 ILE cc_start: 0.6528 (mt) cc_final: 0.5844 (pt)
REVERT: R  322 ARG cc_start: 0.6034 (mtt180) cc_final: 0.5792 (mtm-85)
REVERT: R  345 GLN cc_start: 0.6997 (OUTLIER) cc_final: 0.6745 (mp-120)
REVERT: L    8 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.7117 (mmt)
REVERT: L   14 ARG cc_start: 0.5829 (ptm-80) cc_final: 0.5432 (ppt170)
  outliers start: 28
  outliers final: 13
  residues processed: 168
  average time/residue: 0.6187
  time to fit residues: 109.8839
Evaluate side-chains
  159 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 143
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue  162 SER
Chi-restraints excluded: chain E residue  195 LEU
Chi-restraints excluded: chain R residue  209 ASP
Chi-restraints excluded: chain R residue  267 LEU
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  345 GLN
Chi-restraints excluded: chain L residue    8 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 76 optimal weight:    0.0770
   chunk 84 optimal weight:    0.0170
   chunk 57 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0980
   chunk 21 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 43 optimal weight:    0.0770
   chunk 94 optimal weight:    2.9990
   overall best weight:    0.2334

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
B 175 GLN
B 176 GLN
B 268 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.195148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.137960 restraints weight = 9468.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 1.89
r_work: 0.3461 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3346 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.2654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9158  Z= 0.099
  Angle     :  0.489   8.332  12432  Z= 0.254
  Chirality :  0.041   0.149   1426
  Planarity :  0.003   0.048   1571
  Dihedral  :  4.728  46.618   1262
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 16.01 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 aren not related in a simple way.
  whole:  1.13 (0.25), residues: 1144
  helix:  2.23 (0.27), residues: 385
  sheet:  0.36 (0.29), residues: 278
  loop : -0.17 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  11 
 TYR   0.012   0.001   TYR E 190 
 PHE   0.009   0.001   PHE B 199 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 9154)
  covalent geometry    : angle       0.48850 (12424)
  SS BOND              : bond        0.00158 (    4)
  SS BOND              : angle       0.52594 (    8)
  hydrogen bonds       : bond        0.03582 (  448)
  hydrogen bonds       : angle       4.54062 ( 1263)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 149
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8035 (mttt) cc_final: 0.7297 (mmtm)
REVERT: A   18 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7369 (ttm)
REVERT: A   21 ARG cc_start: 0.7332 (ttm170) cc_final: 0.6999 (mtm110)
REVERT: A   22 ASN cc_start: 0.7635 (m-40) cc_final: 0.7355 (m110)
REVERT: A   28 GLU cc_start: 0.6659 (mt-10) cc_final: 0.5754 (mm-30)
REVERT: A   29 LYS cc_start: 0.8237 (tttt) cc_final: 0.7415 (ttmm)
REVERT: A  186 GLU cc_start: 0.8241 (tt0) cc_final: 0.7531 (mt-10)
REVERT: A  207 GLU cc_start: 0.6476 (tp30) cc_final: 0.6149 (tt0)
REVERT: A  208 ARG cc_start: 0.7816 (ttm-80) cc_final: 0.7187 (ttp80)
REVERT: A  275 GLU cc_start: 0.8315 (tm-30) cc_final: 0.8091 (tp30)
REVERT: A  330 LYS cc_start: 0.6558 (mttt) cc_final: 0.5473 (tttm)
REVERT: A  349 LYS cc_start: 0.7525 (mttt) cc_final: 0.7110 (mtmt)
REVERT: B   42 ARG cc_start: 0.7222 (tpt170) cc_final: 0.6814 (tmt170)
REVERT: B   46 ARG cc_start: 0.7951 (mtp-110) cc_final: 0.7485 (mtm-85)
REVERT: B   52 ARG cc_start: 0.8640 (mtt-85) cc_final: 0.8264 (mtt90)
REVERT: B  129 ARG cc_start: 0.8042 (mtp180) cc_final: 0.7353 (ttt90)
REVERT: B  153 ASP cc_start: 0.8764 (p0) cc_final: 0.8456 (p0)
REVERT: B  221 THR cc_start: 0.7922 (m) cc_final: 0.7708 (m)
REVERT: B  226 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7305 (mp0)
REVERT: B  241 PHE cc_start: 0.8993 (p90) cc_final: 0.8637 (p90)
REVERT: C   21 MET cc_start: 0.7516 (mmm) cc_final: 0.7059 (ttm)
REVERT: C   37 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6978 (tp)
REVERT: C   47 GLU cc_start: 0.7260 (pt0) cc_final: 0.6636 (pm20)
REVERT: E   34 MET cc_start: 0.8314 (mmp) cc_final: 0.8093 (mmm)
REVERT: E  186 GLN cc_start: 0.8454 (tt0) cc_final: 0.8100 (tm-30)
REVERT: R  163 LEU cc_start: 0.6570 (mt) cc_final: 0.6229 (mt)
REVERT: R  165 MET cc_start: 0.5562 (ttt) cc_final: 0.5259 (tpt)
REVERT: R  208 ILE cc_start: 0.6549 (mt) cc_final: 0.5953 (pt)
REVERT: R  322 ARG cc_start: 0.5873 (mtt180) cc_final: 0.5589 (mtm-85)
REVERT: R  345 GLN cc_start: 0.6716 (OUTLIER) cc_final: 0.6432 (mm-40)
REVERT: L    8 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.7212 (mmt)
  outliers start: 30
  outliers final: 12
  residues processed: 167
  average time/residue: 0.5446
  time to fit residues: 96.5620
Evaluate side-chains
  154 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 138
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue  162 SER
Chi-restraints excluded: chain E residue  195 LEU
Chi-restraints excluded: chain R residue  209 ASP
Chi-restraints excluded: chain R residue  267 LEU
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  345 GLN
Chi-restraints excluded: chain L residue    8 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 84 optimal weight:    0.3980
   chunk 75 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 109 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 94 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 108 optimal weight:    9.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
B 268 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.190423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.134588 restraints weight = 9453.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 2.09
r_work: 0.3418 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.2581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9158  Z= 0.168
  Angle     :  0.551   8.908  12432  Z= 0.285
  Chirality :  0.044   0.209   1426
  Planarity :  0.004   0.047   1571
  Dihedral  :  5.033  48.443   1262
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 17.25 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 aren not related in a simple way.
  whole:  1.03 (0.25), residues: 1144
  helix:  2.24 (0.27), residues: 380
  sheet:  0.13 (0.29), residues: 288
  loop : -0.17 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L  14 
 TYR   0.010   0.001   TYR R 297 
 PHE   0.012   0.001   PHE R 150 
 TRP   0.016   0.002   TRP B 169 
 HIS   0.006   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 9154)
  covalent geometry    : angle       0.55064 (12424)
  SS BOND              : bond        0.00234 (    4)
  SS BOND              : angle       0.97283 (    8)
  hydrogen bonds       : bond        0.04023 (  448)
  hydrogen bonds       : angle       4.81566 ( 1263)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 142
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8144 (mttt) cc_final: 0.7560 (mmtm)
REVERT: A   21 ARG cc_start: 0.7411 (ttm170) cc_final: 0.7128 (mtm110)
REVERT: A   22 ASN cc_start: 0.7780 (m-40) cc_final: 0.7491 (m110)
REVERT: A   28 GLU cc_start: 0.6864 (mt-10) cc_final: 0.6004 (mm-30)
REVERT: A   29 LYS cc_start: 0.8315 (tttt) cc_final: 0.7182 (mtmt)
REVERT: A  186 GLU cc_start: 0.8321 (tt0) cc_final: 0.7589 (mt-10)
REVERT: A  207 GLU cc_start: 0.6656 (tp30) cc_final: 0.6269 (mt-10)
REVERT: A  208 ARG cc_start: 0.7876 (ttm-80) cc_final: 0.7244 (ttp80)
REVERT: A  330 LYS cc_start: 0.6664 (mttt) cc_final: 0.5565 (tttm)
REVERT: A  349 LYS cc_start: 0.7571 (mttt) cc_final: 0.7236 (mttt)
REVERT: B   42 ARG cc_start: 0.7227 (tpt170) cc_final: 0.6790 (tmt170)
REVERT: B   46 ARG cc_start: 0.8138 (mtp-110) cc_final: 0.7664 (mtm-85)
REVERT: B   52 ARG cc_start: 0.8679 (mtt-85) cc_final: 0.8301 (mtt90)
REVERT: B  129 ARG cc_start: 0.8090 (mtp180) cc_final: 0.7465 (ttt90)
REVERT: B  221 THR cc_start: 0.8004 (m) cc_final: 0.7746 (m)
REVERT: B  226 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7351 (mm-30)
REVERT: B  241 PHE cc_start: 0.9094 (p90) cc_final: 0.8783 (p90)
REVERT: C   21 MET cc_start: 0.7502 (mmm) cc_final: 0.7024 (ttm)
REVERT: C   47 GLU cc_start: 0.7391 (pt0) cc_final: 0.6717 (pm20)
REVERT: E    6 GLU cc_start: 0.7955 (mp0) cc_final: 0.7748 (mp0)
REVERT: E  186 GLN cc_start: 0.8512 (tt0) cc_final: 0.8147 (tm-30)
REVERT: R  163 LEU cc_start: 0.6692 (mt) cc_final: 0.6324 (mt)
REVERT: R  192 ASP cc_start: 0.5433 (OUTLIER) cc_final: 0.4470 (t70)
REVERT: R  208 ILE cc_start: 0.6721 (mt) cc_final: 0.6011 (pt)
REVERT: R  280 TYR cc_start: 0.6299 (OUTLIER) cc_final: 0.6028 (p90)
REVERT: R  322 ARG cc_start: 0.6094 (mtt180) cc_final: 0.5774 (mtm-85)
REVERT: R  345 GLN cc_start: 0.6846 (OUTLIER) cc_final: 0.6531 (mm110)
REVERT: L    8 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7214 (mmt)
REVERT: L   14 ARG cc_start: 0.6231 (ttp80) cc_final: 0.5431 (ppt170)
  outliers start: 31
  outliers final: 11
  residues processed: 157
  average time/residue: 0.6025
  time to fit residues: 100.3581
Evaluate side-chains
  149 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 134
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain E residue  162 SER
Chi-restraints excluded: chain E residue  166 LEU
Chi-restraints excluded: chain E residue  195 LEU
Chi-restraints excluded: chain R residue  192 ASP
Chi-restraints excluded: chain R residue  209 ASP
Chi-restraints excluded: chain R residue  267 LEU
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  345 GLN
Chi-restraints excluded: chain L residue    8 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 83 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9980
   chunk 102 optimal weight:    2.9990
   chunk 79 optimal weight:    0.3980
   chunk 108 optimal weight:    3.9990
   chunk 14 optimal weight:    0.2980
   chunk 30 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 24 optimal weight:    5.9990
   chunk 2 optimal weight:    0.8980
   chunk 73 optimal weight:    0.1980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
B 268 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.192550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.138353 restraints weight = 9505.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 1.93
r_work: 0.3453 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9158  Z= 0.113
  Angle     :  0.512   9.940  12432  Z= 0.263
  Chirality :  0.042   0.181   1426
  Planarity :  0.003   0.047   1571
  Dihedral  :  4.797  45.390   1262
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 17.77 %
    Favored  : 79.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 aren not related in a simple way.
  whole:  1.09 (0.25), residues: 1144
  helix:  2.22 (0.27), residues: 382
  sheet:  0.26 (0.29), residues: 295
  loop : -0.16 (0.29), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  11 
 TYR   0.011   0.001   TYR E 190 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 9154)
  covalent geometry    : angle       0.51215 (12424)
  SS BOND              : bond        0.00184 (    4)
  SS BOND              : angle       0.71782 (    8)
  hydrogen bonds       : bond        0.03624 (  448)
  hydrogen bonds       : angle       4.65252 ( 1263)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 138
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8114 (mttt) cc_final: 0.7498 (mmtm)
REVERT: A   21 ARG cc_start: 0.7383 (ttm170) cc_final: 0.7117 (mtm110)
REVERT: A   22 ASN cc_start: 0.7770 (m-40) cc_final: 0.7469 (m110)
REVERT: A   28 GLU cc_start: 0.6755 (mt-10) cc_final: 0.5860 (mm-30)
REVERT: A   29 LYS cc_start: 0.8299 (tttt) cc_final: 0.7472 (ttmm)
REVERT: A   32 ARG cc_start: 0.7481 (mtp180) cc_final: 0.7276 (mtm-85)
REVERT: A   53 MET cc_start: 0.7064 (mtt) cc_final: 0.6518 (mtm)
REVERT: A  186 GLU cc_start: 0.8266 (tt0) cc_final: 0.7579 (mt-10)
REVERT: A  208 ARG cc_start: 0.7774 (ttm-80) cc_final: 0.7118 (ttp80)
REVERT: A  251 ASP cc_start: 0.7731 (p0) cc_final: 0.7236 (t0)
REVERT: A  275 GLU cc_start: 0.8292 (tm-30) cc_final: 0.8055 (tp30)
REVERT: A  283 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6552 (tt)
REVERT: A  330 LYS cc_start: 0.6590 (mttt) cc_final: 0.5470 (tttm)
REVERT: A  349 LYS cc_start: 0.7555 (mttt) cc_final: 0.7149 (mtmt)
REVERT: B   42 ARG cc_start: 0.7195 (tpt170) cc_final: 0.6769 (tmt170)
REVERT: B   46 ARG cc_start: 0.8089 (mtp-110) cc_final: 0.7648 (mtm-85)
REVERT: B   52 ARG cc_start: 0.8678 (mtt-85) cc_final: 0.8312 (mtt90)
REVERT: B  129 ARG cc_start: 0.8070 (mtp180) cc_final: 0.7453 (ttt90)
REVERT: B  221 THR cc_start: 0.7957 (m) cc_final: 0.7711 (m)
REVERT: B  226 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7386 (mp0)
REVERT: B  241 PHE cc_start: 0.9022 (p90) cc_final: 0.8684 (p90)
REVERT: C   21 MET cc_start: 0.7495 (mmm) cc_final: 0.7016 (ttm)
REVERT: C   47 GLU cc_start: 0.7324 (pt0) cc_final: 0.6615 (pm20)
REVERT: E  186 GLN cc_start: 0.8504 (tt0) cc_final: 0.8158 (tm-30)
REVERT: R  122 LEU cc_start: 0.6941 (mt) cc_final: 0.6733 (mp)
REVERT: R  163 LEU cc_start: 0.6668 (mt) cc_final: 0.6270 (mt)
REVERT: R  165 MET cc_start: 0.5329 (OUTLIER) cc_final: 0.4847 (tpt)
REVERT: R  173 MET cc_start: 0.6253 (mmt) cc_final: 0.5719 (ptm)
REVERT: R  208 ILE cc_start: 0.6647 (mt) cc_final: 0.5943 (pt)
REVERT: R  209 ASP cc_start: 0.6632 (OUTLIER) cc_final: 0.6329 (t0)
REVERT: R  280 TYR cc_start: 0.6233 (OUTLIER) cc_final: 0.5964 (p90)
REVERT: R  322 ARG cc_start: 0.5941 (mtt180) cc_final: 0.5638 (mtm-85)
REVERT: R  345 GLN cc_start: 0.6775 (OUTLIER) cc_final: 0.6558 (mm-40)
REVERT: L    8 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7382 (tpp)
REVERT: L   14 ARG cc_start: 0.6305 (ttp80) cc_final: 0.5846 (ppt170)
  outliers start: 25
  outliers final: 14
  residues processed: 150
  average time/residue: 0.6329
  time to fit residues: 100.5156
Evaluate side-chains
  155 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 135
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  162 SER
Chi-restraints excluded: chain E residue  166 LEU
Chi-restraints excluded: chain E residue  195 LEU
Chi-restraints excluded: chain R residue  165 MET
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  209 ASP
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  345 GLN
Chi-restraints excluded: chain L residue    8 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 31 optimal weight:    0.0980
   chunk 39 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 103 optimal weight:    0.8980
   chunk 69 optimal weight:    0.5980
   chunk 58 optimal weight:    0.4980
   chunk 91 optimal weight:    0.5980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN
B 268 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.192534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.138811 restraints weight = 9501.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 1.96
r_work: 0.3448 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3329 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9158  Z= 0.117
  Angle     :  0.514   8.998  12432  Z= 0.263
  Chirality :  0.042   0.167   1426
  Planarity :  0.004   0.047   1571
  Dihedral  :  4.728  44.036   1262
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 18.29 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 aren not related in a simple way.
  whole:  1.09 (0.25), residues: 1144
  helix:  2.27 (0.27), residues: 382
  sheet:  0.23 (0.29), residues: 290
  loop : -0.16 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L  11 
 TYR   0.011   0.001   TYR E 190 
 PHE   0.010   0.001   PHE B 199 
 TRP   0.015   0.001   TRP R 338 
 HIS   0.004   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 9154)
  covalent geometry    : angle       0.51361 (12424)
  SS BOND              : bond        0.00197 (    4)
  SS BOND              : angle       0.84783 (    8)
  hydrogen bonds       : bond        0.03588 (  448)
  hydrogen bonds       : angle       4.61840 ( 1263)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 133
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8096 (mttt) cc_final: 0.7468 (mmtm)
REVERT: A   21 ARG cc_start: 0.7388 (ttm170) cc_final: 0.7134 (mtm110)
REVERT: A   22 ASN cc_start: 0.7768 (m-40) cc_final: 0.7475 (m110)
REVERT: A   28 GLU cc_start: 0.6754 (mt-10) cc_final: 0.5865 (mm-30)
REVERT: A   29 LYS cc_start: 0.8315 (tttt) cc_final: 0.7491 (ttmm)
REVERT: A   53 MET cc_start: 0.7093 (mtt) cc_final: 0.6544 (mtm)
REVERT: A  186 GLU cc_start: 0.8288 (tt0) cc_final: 0.7600 (mt-10)
REVERT: A  208 ARG cc_start: 0.7778 (ttm-80) cc_final: 0.7187 (ttp80)
REVERT: A  251 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7345 (t0)
REVERT: A  283 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6684 (tt)
REVERT: A  330 LYS cc_start: 0.6682 (mttt) cc_final: 0.5526 (tttm)
REVERT: A  349 LYS cc_start: 0.7565 (mttt) cc_final: 0.7107 (mtmt)
REVERT: B   42 ARG cc_start: 0.7203 (tpt170) cc_final: 0.6788 (tmt170)
REVERT: B   46 ARG cc_start: 0.8151 (mtp-110) cc_final: 0.7709 (mtm-85)
REVERT: B   52 ARG cc_start: 0.8678 (mtt-85) cc_final: 0.8325 (mtt90)
REVERT: B  129 ARG cc_start: 0.8091 (mtp180) cc_final: 0.7463 (ttt90)
REVERT: B  221 THR cc_start: 0.7965 (m) cc_final: 0.7702 (m)
REVERT: B  226 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7379 (mp0)
REVERT: B  241 PHE cc_start: 0.9015 (p90) cc_final: 0.8691 (p90)
REVERT: C   21 MET cc_start: 0.7520 (mmm) cc_final: 0.7010 (ttm)
REVERT: C   47 GLU cc_start: 0.7335 (pt0) cc_final: 0.6713 (pm20)
REVERT: E  186 GLN cc_start: 0.8513 (tt0) cc_final: 0.8171 (tm-30)
REVERT: R  163 LEU cc_start: 0.6692 (mt) cc_final: 0.6335 (mt)
REVERT: R  165 MET cc_start: 0.5412 (OUTLIER) cc_final: 0.4809 (tpt)
REVERT: R  173 MET cc_start: 0.6332 (mmt) cc_final: 0.5957 (ptm)
REVERT: R  208 ILE cc_start: 0.6790 (mt) cc_final: 0.6087 (pt)
REVERT: R  209 ASP cc_start: 0.6638 (OUTLIER) cc_final: 0.6343 (t0)
REVERT: R  280 TYR cc_start: 0.6247 (OUTLIER) cc_final: 0.5991 (p90)
REVERT: R  322 ARG cc_start: 0.5934 (mtt180) cc_final: 0.5635 (mtm-85)
REVERT: L   14 ARG cc_start: 0.6324 (ttp80) cc_final: 0.5744 (ppt170)
  outliers start: 26
  outliers final: 15
  residues processed: 145
  average time/residue: 0.5988
  time to fit residues: 92.0291
Evaluate side-chains
  153 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  162 SER
Chi-restraints excluded: chain E residue  166 LEU
Chi-restraints excluded: chain E residue  195 LEU
Chi-restraints excluded: chain R residue  165 MET
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  209 ASP
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  320 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 60 optimal weight:    0.8980
   chunk 16 optimal weight:    7.9990
   chunk 39 optimal weight:    0.5980
   chunk 77 optimal weight:    0.0870
   chunk 48 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 80 optimal weight:    1.9990
   chunk 109 optimal weight:    1.9990
   chunk 88 optimal weight:    6.9990
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN
R 348 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.193103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.138944 restraints weight = 9426.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 1.93
r_work: 0.3447 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3328 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.2821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9158  Z= 0.128
  Angle     :  0.530  12.487  12432  Z= 0.270
  Chirality :  0.042   0.172   1426
  Planarity :  0.004   0.059   1571
  Dihedral  :  4.467  43.303   1259
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 18.49 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 aren not related in a simple way.
  whole:  1.07 (0.25), residues: 1144
  helix:  2.25 (0.27), residues: 383
  sheet:  0.20 (0.29), residues: 292
  loop : -0.18 (0.29), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.000   ARG R 299 
 TYR   0.010   0.001   TYR E 190 
 PHE   0.010   0.001   PHE B 199 
 TRP   0.015   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 9154)
  covalent geometry    : angle       0.52961 (12424)
  SS BOND              : bond        0.00213 (    4)
  SS BOND              : angle       0.63926 (    8)
  hydrogen bonds       : bond        0.03671 (  448)
  hydrogen bonds       : angle       4.64358 ( 1263)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 135
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8078 (mttt) cc_final: 0.7442 (mmtm)
REVERT: A   21 ARG cc_start: 0.7357 (ttm170) cc_final: 0.7096 (mtm110)
REVERT: A   22 ASN cc_start: 0.7759 (m-40) cc_final: 0.7461 (m110)
REVERT: A   28 GLU cc_start: 0.6750 (mt-10) cc_final: 0.5847 (mm-30)
REVERT: A   29 LYS cc_start: 0.8309 (tttt) cc_final: 0.7467 (ttmm)
REVERT: A   53 MET cc_start: 0.7138 (mtt) cc_final: 0.6615 (mtm)
REVERT: A  186 GLU cc_start: 0.8279 (tt0) cc_final: 0.7597 (mt-10)
REVERT: A  208 ARG cc_start: 0.7767 (ttm-80) cc_final: 0.7131 (ttp80)
REVERT: A  251 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7326 (t0)
REVERT: A  275 GLU cc_start: 0.8261 (tm-30) cc_final: 0.8032 (tp30)
REVERT: A  283 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6614 (tt)
REVERT: A  330 LYS cc_start: 0.6647 (mttt) cc_final: 0.5481 (tttm)
REVERT: A  349 LYS cc_start: 0.7553 (mttt) cc_final: 0.7093 (mtmt)
REVERT: B   42 ARG cc_start: 0.7160 (tpt170) cc_final: 0.6770 (tmt170)
REVERT: B   46 ARG cc_start: 0.8165 (mtp-110) cc_final: 0.7669 (mtm-85)
REVERT: B   52 ARG cc_start: 0.8569 (mtt-85) cc_final: 0.8294 (mtt90)
REVERT: B  129 ARG cc_start: 0.8076 (mtp180) cc_final: 0.7443 (ttt90)
REVERT: B  221 THR cc_start: 0.7966 (m) cc_final: 0.7703 (m)
REVERT: B  226 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7358 (mp0)
REVERT: B  241 PHE cc_start: 0.9024 (p90) cc_final: 0.8659 (p90)
REVERT: C   21 MET cc_start: 0.7537 (mmm) cc_final: 0.7045 (ttm)
REVERT: C   47 GLU cc_start: 0.7354 (pt0) cc_final: 0.6631 (pm20)
REVERT: E   34 MET cc_start: 0.8684 (mmm) cc_final: 0.8461 (mmp)
REVERT: E   46 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7599 (tt0)
REVERT: E  186 GLN cc_start: 0.8497 (tt0) cc_final: 0.8140 (tm-30)
REVERT: R  163 LEU cc_start: 0.6740 (mt) cc_final: 0.6378 (mt)
REVERT: R  165 MET cc_start: 0.5466 (OUTLIER) cc_final: 0.4850 (tpt)
REVERT: R  173 MET cc_start: 0.6287 (mmt) cc_final: 0.5925 (ptm)
REVERT: R  192 ASP cc_start: 0.5414 (OUTLIER) cc_final: 0.4475 (t70)
REVERT: R  208 ILE cc_start: 0.6737 (mt) cc_final: 0.6036 (pt)
REVERT: R  209 ASP cc_start: 0.6813 (OUTLIER) cc_final: 0.6527 (t0)
REVERT: R  322 ARG cc_start: 0.5940 (mtt180) cc_final: 0.5633 (mtm-85)
REVERT: L   14 ARG cc_start: 0.6318 (ttp80) cc_final: 0.5855 (ppt170)
  outliers start: 26
  outliers final: 16
  residues processed: 150
  average time/residue: 0.5686
  time to fit residues: 90.3189
Evaluate side-chains
  157 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 135
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  162 SER
Chi-restraints excluded: chain E residue  166 LEU
Chi-restraints excluded: chain R residue  165 MET
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  192 ASP
Chi-restraints excluded: chain R residue  209 ASP
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  320 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 17 optimal weight:    0.3980
   chunk 21 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 111 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 64 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN
E 113 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.191697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.137323 restraints weight = 9494.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 2.14
r_work: 0.3431 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3312 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.2843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9158  Z= 0.133
  Angle     :  0.533   9.195  12432  Z= 0.272
  Chirality :  0.043   0.151   1426
  Planarity :  0.004   0.047   1571
  Dihedral  :  4.495  42.463   1259
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 18.39 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 aren not related in a simple way.
  whole:  1.08 (0.25), residues: 1144
  helix:  2.32 (0.27), residues: 377
  sheet:  0.21 (0.29), residues: 290
  loop : -0.20 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG L  11 
 TYR   0.010   0.001   TYR E 190 
 PHE   0.010   0.001   PHE B 199 
 TRP   0.015   0.002   TRP B 169 
 HIS   0.004   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 9154)
  covalent geometry    : angle       0.53251 (12424)
  SS BOND              : bond        0.00196 (    4)
  SS BOND              : angle       0.67572 (    8)
  hydrogen bonds       : bond        0.03710 (  448)
  hydrogen bonds       : angle       4.67112 ( 1263)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 131
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8146 (mttt) cc_final: 0.7521 (mmtm)
REVERT: A   21 ARG cc_start: 0.7419 (ttm170) cc_final: 0.7154 (mtm110)
REVERT: A   22 ASN cc_start: 0.7777 (m-40) cc_final: 0.7479 (m110)
REVERT: A   28 GLU cc_start: 0.6758 (mt-10) cc_final: 0.5849 (mm-30)
REVERT: A   29 LYS cc_start: 0.8301 (tttt) cc_final: 0.7469 (ttmm)
REVERT: A   53 MET cc_start: 0.7171 (mtt) cc_final: 0.6649 (mtm)
REVERT: A  186 GLU cc_start: 0.8317 (tt0) cc_final: 0.7615 (mt-10)
REVERT: A  208 ARG cc_start: 0.7763 (ttm-80) cc_final: 0.7005 (ttp80)
REVERT: A  251 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7322 (t0)
REVERT: A  275 GLU cc_start: 0.8267 (tm-30) cc_final: 0.8030 (tp30)
REVERT: A  283 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6643 (tt)
REVERT: A  330 LYS cc_start: 0.6671 (mttt) cc_final: 0.5514 (tttm)
REVERT: A  349 LYS cc_start: 0.7577 (mttt) cc_final: 0.7114 (mtmt)
REVERT: B   42 ARG cc_start: 0.7169 (tpt170) cc_final: 0.6771 (tmt170)
REVERT: B   46 ARG cc_start: 0.8182 (mtp-110) cc_final: 0.7683 (mtm-85)
REVERT: B   52 ARG cc_start: 0.8576 (mtt-85) cc_final: 0.8298 (mtt90)
REVERT: B  129 ARG cc_start: 0.8075 (mtp180) cc_final: 0.7440 (ttt90)
REVERT: B  221 THR cc_start: 0.7989 (m) cc_final: 0.7738 (m)
REVERT: B  226 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7366 (mp0)
REVERT: C   21 MET cc_start: 0.7535 (mmm) cc_final: 0.7021 (ttm)
REVERT: C   47 GLU cc_start: 0.7384 (pt0) cc_final: 0.6694 (pm20)
REVERT: E   46 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7623 (tt0)
REVERT: E  186 GLN cc_start: 0.8566 (tt0) cc_final: 0.8212 (tm-30)
REVERT: R  122 LEU cc_start: 0.7098 (mp) cc_final: 0.6878 (mp)
REVERT: R  163 LEU cc_start: 0.6764 (mt) cc_final: 0.6458 (mt)
REVERT: R  173 MET cc_start: 0.6285 (mmt) cc_final: 0.5930 (ptm)
REVERT: R  192 ASP cc_start: 0.5424 (OUTLIER) cc_final: 0.4495 (t70)
REVERT: R  208 ILE cc_start: 0.6846 (mt) cc_final: 0.6098 (pt)
REVERT: R  209 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6118 (t0)
REVERT: R  280 TYR cc_start: 0.6275 (OUTLIER) cc_final: 0.6035 (p90)
REVERT: R  322 ARG cc_start: 0.5987 (mtt180) cc_final: 0.5663 (mtm-85)
REVERT: L   14 ARG cc_start: 0.6311 (ttp80) cc_final: 0.5837 (ppt170)
  outliers start: 26
  outliers final: 14
  residues processed: 145
  average time/residue: 0.5902
  time to fit residues: 90.9639
Evaluate side-chains
  149 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  162 SER
Chi-restraints excluded: chain E residue  166 LEU
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  192 ASP
Chi-restraints excluded: chain R residue  209 ASP
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  308 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 94 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 92 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 110 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.192363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.138185 restraints weight = 9348.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 1.99
r_work: 0.3438 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3319 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.2856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9158  Z= 0.141
  Angle     :  0.546  13.105  12432  Z= 0.277
  Chirality :  0.043   0.219   1426
  Planarity :  0.004   0.076   1571
  Dihedral  :  4.543  42.062   1259
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 18.49 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 aren not related in a simple way.
  whole:  1.07 (0.25), residues: 1144
  helix:  2.31 (0.27), residues: 377
  sheet:  0.19 (0.29), residues: 290
  loop : -0.20 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG R 299 
 TYR   0.019   0.001   TYR A 296 
 PHE   0.010   0.001   PHE A 196 
 TRP   0.016   0.002   TRP B 169 
 HIS   0.004   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 9154)
  covalent geometry    : angle       0.54549 (12424)
  SS BOND              : bond        0.00251 (    4)
  SS BOND              : angle       0.79743 (    8)
  hydrogen bonds       : bond        0.03768 (  448)
  hydrogen bonds       : angle       4.69557 ( 1263)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3788.41 seconds
wall clock time: 65 minutes 15.07 seconds (3915.07 seconds total)