Starting phenix.real_space_refine
on Thu Sep 18 12:56:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9o12_49995/09_2025/9o12_49995.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9o12_49995/09_2025/9o12_49995.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9o12_49995/09_2025/9o12_49995.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9o12_49995/09_2025/9o12_49995.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9o12_49995/09_2025/9o12_49995.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9o12_49995/09_2025/9o12_49995.cif"
  }
  resolution = 4.3
  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=   0.002 sd=   0.012
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: 5
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    5520      2.51       5
     N    1356      2.21       5
     O    1444      1.98       5
     H    8772      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17136
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 4284
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 10, 'TRANS': 250}
    Chain: "B"
      Number of atoms: 4284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 4284
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 10, 'TRANS': 250}
    Chain: "C"
      Number of atoms: 4284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 4284
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 10, 'TRANS': 250}
    Chain: "D"
      Number of atoms: 4284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 4284
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 10, 'TRANS': 250}
  Time building chain proxies: 3.10, per 1000 atoms: 0.18
  Number of scatterers: 17136
  At special positions: 0
  Unit cell: (118.137, 122.595, 78.758, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      44     16.00
     O    1444      8.00
     N    1356      7.00
     C    5520      6.00
     H    8772      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.51
  Conformation dependent library (CDL) restraints added in 438.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1992

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 2 sheets defined
      81.7% alpha, 0.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 169 through 181
      removed outlier: 4.182A  pdb=" N   LYS A 174 " --> pdb=" O   GLU A 170 " (cutoff:3.500A)
      removed outlier: 5.265A  pdb=" N   LEU A 175 " --> pdb=" O   LYS A 171 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   LEU A 178 " --> pdb=" O   LYS A 174 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   LEU A 179 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 208
    Processing helix  chain 'A' and resid 209 through 211
      No H-bonds generated for 'chain 'A' and resid 209 through 211'
    Processing helix  chain 'A' and resid 226 through 251
    Processing helix  chain 'A' and resid 253 through 259
    Processing helix  chain 'A' and resid 260 through 280
      removed outlier: 3.564A  pdb=" N   ILE A 270 " --> pdb=" O   ASP A 266 " (cutoff:3.500A)
      Proline residue:  A 272  - end of helix
    Processing helix  chain 'A' and resid 288 through 302
    Processing helix  chain 'A' and resid 303 through 313
    Processing helix  chain 'A' and resid 314 through 354
      removed outlier: 3.729A  pdb=" N   GLN A 318 " --> pdb=" O   SER A 314 " (cutoff:3.500A)
      removed outlier: 5.178A  pdb=" N   ASN A 329 " --> pdb=" O   ARG A 325 " (cutoff:3.500A)
      removed outlier: 5.531A  pdb=" N   GLU A 330 " --> pdb=" O   ARG A 326 " (cutoff:3.500A)
      removed outlier: 4.605A  pdb=" N   GLY A 332 " --> pdb=" O   TYR A 328 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   LEU A 333 " --> pdb=" O   ASN A 329 " (cutoff:3.500A)
      removed outlier: 4.868A  pdb=" N   LEU A 334 " --> pdb=" O   GLU A 330 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   ILE A 335 " --> pdb=" O   LEU A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 376
      removed outlier: 4.491A  pdb=" N   TRP A 369 " --> pdb=" O   PRO A 365 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   TRP A 370 " --> pdb=" O   ALA A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 407
      removed outlier: 3.795A  pdb=" N   ILE A 399 " --> pdb=" O   GLY A 395 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   LEU A 407 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 425
      removed outlier: 3.663A  pdb=" N   ILE A 412 " --> pdb=" O   PRO A 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 181
      removed outlier: 4.227A  pdb=" N   ARG B 172 " --> pdb=" O   CYS B 168 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   LYS B 174 " --> pdb=" O   GLU B 170 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   LEU B 175 " --> pdb=" O   LYS B 171 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   LEU B 178 " --> pdb=" O   LYS B 174 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LEU B 179 " --> pdb=" O   LEU B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 209
      removed outlier: 4.098A  pdb=" N   LEU B 191 " --> pdb=" O   ALA B 187 " (cutoff:3.500A)
      removed outlier: 4.605A  pdb=" N   ILE B 196 " --> pdb=" O   ALA B 192 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   PHE B 198 " --> pdb=" O   ILE B 194 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ILE B 199 " --> pdb=" O   SER B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 226 through 250
    Processing helix  chain 'B' and resid 253 through 260
      removed outlier: 3.733A  pdb=" N   PHE B 258 " --> pdb=" O   LYS B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 280
      removed outlier: 4.637A  pdb=" N   ASP B 266 " --> pdb=" O   LEU B 262 " (cutoff:3.500A)
      Proline residue:  B 272  - end of helix
      removed outlier: 4.109A  pdb=" N   THR B 276 " --> pdb=" O   PRO B 272 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   ILE B 277 " --> pdb=" O   TYR B 273 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   PHE B 278 " --> pdb=" O   TYR B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 300
      removed outlier: 3.870A  pdb=" N   ARG B 293 " --> pdb=" O   PHE B 289 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   ARG B 294 " --> pdb=" O   GLN B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 309
      removed outlier: 4.171A  pdb=" N   ILE B 304 " --> pdb=" O   ILE B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 315 through 327
      removed outlier: 4.406A  pdb=" N   ARG B 325 " --> pdb=" O   GLY B 321 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ARG B 326 " --> pdb=" O   PHE B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 354
      removed outlier: 4.538A  pdb=" N   GLY B 332 " --> pdb=" O   TYR B 328 " (cutoff:3.500A)
      removed outlier: 5.367A  pdb=" N   LEU B 333 " --> pdb=" O   ASN B 329 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   LEU B 334 " --> pdb=" O   GLU B 330 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ILE B 335 " --> pdb=" O   LEU B 331 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   PHE B 351 " --> pdb=" O   SER B 347 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ALA B 352 " --> pdb=" O   LEU B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 366
      No H-bonds generated for 'chain 'B' and resid 364 through 366'
    Processing helix  chain 'B' and resid 367 through 375
    Processing helix  chain 'B' and resid 387 through 407
      removed outlier: 3.789A  pdb=" N   ILE B 399 " --> pdb=" O   GLY B 395 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LEU B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 408 through 425
      removed outlier: 3.548A  pdb=" N   ILE B 412 " --> pdb=" O   PRO B 408 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 168 through 175
    Processing helix  chain 'C' and resid 175 through 181
    Processing helix  chain 'C' and resid 185 through 209
      removed outlier: 4.017A  pdb=" N   LYS C 189 " --> pdb=" O   SER C 185 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 226 through 250
    Processing helix  chain 'C' and resid 253 through 259
      removed outlier: 3.665A  pdb=" N   LYS C 259 " --> pdb=" O   TRP C 255 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 260 through 280
      Proline residue:  C 272  - end of helix
      removed outlier: 4.128A  pdb=" N   PHE C 278 " --> pdb=" O   TYR C 274 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   THR C 280 " --> pdb=" O   THR C 276 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 281 through 285
    Processing helix  chain 'C' and resid 288 through 299
      removed outlier: 3.958A  pdb=" N   ARG C 294 " --> pdb=" O   GLN C 290 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLN C 297 " --> pdb=" O   ARG C 293 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   PHE C 299 " --> pdb=" O   VAL C 295 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 300 through 314
      removed outlier: 3.882A  pdb=" N   ILE C 304 " --> pdb=" O   ILE C 301 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   LYS C 309 " --> pdb=" O   ARG C 306 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 315 through 354
      removed outlier: 5.583A  pdb=" N   ASN C 329 " --> pdb=" O   ARG C 325 " (cutoff:3.500A)
      removed outlier: 6.002A  pdb=" N   GLU C 330 " --> pdb=" O   ARG C 326 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   LEU C 333 " --> pdb=" O   ASN C 329 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   ILE C 335 " --> pdb=" O   LEU C 331 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ALA C 352 " --> pdb=" O   LEU C 348 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 363 through 375
      removed outlier: 3.872A  pdb=" N   TRP C 369 " --> pdb=" O   PRO C 365 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   TRP C 370 " --> pdb=" O   ALA C 366 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 387 through 407
      removed outlier: 3.676A  pdb=" N   ILE C 399 " --> pdb=" O   GLY C 395 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   VAL C 402 " --> pdb=" O   CYS C 398 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LEU C 407 " --> pdb=" O   LEU C 403 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 408 through 425
      removed outlier: 3.822A  pdb=" N   ILE C 412 " --> pdb=" O   PRO C 408 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 170 through 181
      removed outlier: 3.690A  pdb=" N   LEU D 179 " --> pdb=" O   LEU D 175 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 185 through 209
      removed outlier: 4.060A  pdb=" N   LEU D 191 " --> pdb=" O   ALA D 187 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 210 through 213
      removed outlier: 5.981A  pdb=" N   GLU D 213 " --> pdb=" O   THR D 210 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 210 through 213'
    Processing helix  chain 'D' and resid 226 through 251
    Processing helix  chain 'D' and resid 253 through 260
      removed outlier: 3.806A  pdb=" N   GLY D 260 " --> pdb=" O   LYS D 256 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 260 through 281
      removed outlier: 5.237A  pdb=" N   ASP D 266 " --> pdb=" O   LEU D 262 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   LEU D 267 " --> pdb=" O   ASN D 263 " (cutoff:3.500A)
      Proline residue:  D 272  - end of helix
      removed outlier: 3.776A  pdb=" N   THR D 280 " --> pdb=" O   THR D 276 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 288 through 302
      removed outlier: 3.768A  pdb=" N   VAL D 292 " --> pdb=" O   GLN D 288 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   VAL D 296 " --> pdb=" O   VAL D 292 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLN D 297 " --> pdb=" O   ARG D 293 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 303 through 313
    Processing helix  chain 'D' and resid 314 through 332
      removed outlier: 3.624A  pdb=" N   PHE D 322 " --> pdb=" O   GLN D 318 " (cutoff:3.500A)
      removed outlier: 5.942A  pdb=" N   ASN D 329 " --> pdb=" O   ARG D 325 " (cutoff:3.500A)
      removed outlier: 5.793A  pdb=" N   GLU D 330 " --> pdb=" O   ARG D 326 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 333 through 354
      removed outlier: 3.987A  pdb=" N   SER D 347 " --> pdb=" O   MET D 343 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 363 through 376
      removed outlier: 4.187A  pdb=" N   TRP D 369 " --> pdb=" O   PRO D 365 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   TRP D 370 " --> pdb=" O   ALA D 366 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 387 through 407
      removed outlier: 3.517A  pdb=" N   CYS D 398 " --> pdb=" O   GLY D 394 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   ILE D 399 " --> pdb=" O   GLY D 395 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LEU D 407 " --> pdb=" O   LEU D 403 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 408 through 425
      removed outlier: 3.768A  pdb=" N   ILE D 412 " --> pdb=" O   PRO D 408 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LYS D 421 " --> pdb=" O   SER D 417 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   GLU D 422 " --> pdb=" O   GLU D 418 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   GLN D 423 " --> pdb=" O   PHE D 419 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   LYS D 424 " --> pdb=" O   TYR D 420 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 216 through 217
    Processing sheet with id=AA2, first strand: chain 'D' and resid 215 through 217

    560 hydrogen bonds defined for protein.
    1578 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: 3.48

  Time building geometry restraints manager: 2.07 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 8752
        1.03 -     1.23: 20
        1.23 -     1.42: 3452
        1.42 -     1.61: 5028
        1.61 -     1.81: 68
  Bond restraints: 17320
  Sorted by residual:
  bond pdb=" N   CYS D 167 "
       pdb=" CA  CYS D 167 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.05e+00
  bond pdb=" N   CYS C 167 "
       pdb=" CA  CYS C 167 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.88e+00
  bond pdb=" N   CYS B 167 "
       pdb=" CA  CYS B 167 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.87e+00
  bond pdb=" N   CYS A 167 "
       pdb=" CA  CYS A 167 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.84e+00
  bond pdb=" N   CYS D 167 "
       pdb=" H   CYS D 167 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.27e+00
  ... (remaining 17315 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.92: 28779
        0.92 -     1.83: 2557
        1.83 -     2.75: 109
        2.75 -     3.66: 23
        3.66 -     4.58: 24
  Bond angle restraints: 31492
  Sorted by residual:
  angle pdb=" N   ILE D 364 "
        pdb=" CA  ILE D 364 "
        pdb=" C   ILE D 364 "
      ideal   model   delta    sigma   weight residual
     112.35  108.58    3.77 1.20e+00 6.94e-01 9.86e+00
  angle pdb=" C   ILE B 409 "
        pdb=" CA  ILE B 409 "
        pdb=" CB  ILE B 409 "
      ideal   model   delta    sigma   weight residual
     114.00  110.70    3.30 1.31e+00 5.83e-01 6.34e+00
  angle pdb=" CA  ILE B 409 "
        pdb=" C   ILE B 409 "
        pdb=" N   PRO B 410 "
      ideal   model   delta    sigma   weight residual
     120.83  119.34    1.49 6.10e-01 2.69e+00 5.93e+00
  angle pdb=" CA  ILE D 364 "
        pdb=" C   ILE D 364 "
        pdb=" N   PRO D 365 "
      ideal   model   delta    sigma   weight residual
     120.83  119.56    1.27 6.10e-01 2.69e+00 4.36e+00
  angle pdb=" CA  PHE A 361 "
        pdb=" C   PHE A 361 "
        pdb=" N   LYS A 362 "
      ideal   model   delta    sigma   weight residual
     114.76  117.00   -2.24 1.14e+00 7.69e-01 3.86e+00
  ... (remaining 31487 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.62: 7596
       17.62 -    35.24: 320
       35.24 -    52.85: 99
       52.85 -    70.47: 32
       70.47 -    88.09: 13
  Dihedral angle restraints: 8060
    sinusoidal: 4384
      harmonic: 3676
  Sorted by residual:
  dihedral pdb=" CA  ALA B 406 "
           pdb=" C   ALA B 406 "
           pdb=" N   LEU B 407 "
           pdb=" CA  LEU B 407 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.73  -19.27     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" CA  ALA C 406 "
           pdb=" C   ALA C 406 "
           pdb=" N   LEU C 407 "
           pdb=" CA  LEU C 407 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.93  -19.07     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  ILE B 301 "
           pdb=" C   ILE B 301 "
           pdb=" N   MET B 302 "
           pdb=" CA  MET B 302 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.71  -17.29     0      5.00e+00 4.00e-02 1.20e+01
  ... (remaining 8057 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.023: 874
       0.023 -    0.047: 234
       0.047 -    0.070: 139
       0.070 -    0.094: 91
       0.094 -    0.117: 26
  Chirality restraints: 1364
  Sorted by residual:
  chirality pdb=" CA  PRO C 272 "
            pdb=" N   PRO C 272 "
            pdb=" C   PRO C 272 "
            pdb=" CB  PRO C 272 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.44e-01
  chirality pdb=" CA  PRO B 410 "
            pdb=" N   PRO B 410 "
            pdb=" C   PRO B 410 "
            pdb=" CB  PRO B 410 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.38e-01
  chirality pdb=" CA  PRO A 410 "
            pdb=" N   PRO A 410 "
            pdb=" C   PRO A 410 "
            pdb=" CB  PRO A 410 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.33e-01
  ... (remaining 1361 not shown)

  Planarity restraints: 2408
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 407 "    0.026 5.00e-02 4.00e+02   3.92e-02 2.46e+00
        pdb=" N   PRO A 408 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 408 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 408 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 278 "   -0.011 2.00e-02 2.50e+03   7.05e-03 1.49e+00
        pdb=" CG  PHE A 278 "    0.020 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 278 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 278 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 278 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 278 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 278 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD1 PHE A 278 "    0.000 2.00e-02 2.50e+03
        pdb=" HD2 PHE A 278 "    0.001 2.00e-02 2.50e+03
        pdb=" HE1 PHE A 278 "   -0.001 2.00e-02 2.50e+03
        pdb=" HE2 PHE A 278 "   -0.001 2.00e-02 2.50e+03
        pdb=" HZ  PHE A 278 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 271 "   -0.018 5.00e-02 4.00e+02   2.75e-02 1.21e+00
        pdb=" N   PRO B 272 "    0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO B 272 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B 272 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 2405 not shown)

  Histogram of nonbonded interaction distances:
        1.55 -     2.16: 601
        2.16 -     2.77: 33819
        2.77 -     3.38: 47738
        3.38 -     3.99: 53912
        3.99 -     4.60: 87873
  Nonbonded interactions: 223943
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 353 "
            pdb=" H   LYS B 386 "
     model   vdw
     1.550 2.450
  nonbonded pdb=" OD1 ASN B 226 "
            pdb=" H   LEU B 229 "
     model   vdw
     1.556 2.450
  nonbonded pdb=" O   ILE A 411 "
            pdb="HD21 ASN A 415 "
     model   vdw
     1.570 2.450
  nonbonded pdb=" OE1 GLU D 330 "
            pdb=" H   GLU D 330 "
     model   vdw
     1.573 2.450
  nonbonded pdb=" O   LEU C 211 "
            pdb=" H   GLN C 215 "
     model   vdw
     1.582 2.450
  ... (remaining 223938 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.400
  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:             0.090
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     15.560
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7199
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8548  Z= 0.140
  Angle     :  0.473   4.538  11572  Z= 0.275
  Chirality :  0.036   0.117   1364
  Planarity :  0.003   0.039   1408
  Dihedral  : 10.075  88.089   3140
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  :  2.05 %
    Favored  : 96.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.53 (0.28), residues: 1036
  helix:  1.61 (0.20), residues: 753
  sheet:  None (None), residues: 0
  loop : -0.51 (0.42), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 312 
 TYR   0.008   0.001   TYR B 328 
 PHE   0.021   0.001   PHE A 278 
 TRP   0.010   0.001   TRP A 239 
 HIS   0.003   0.001   HIS C 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 8548)
  covalent geometry    : angle       0.47304 (11572)
  hydrogen bonds       : bond        0.15750 (  560)
  hydrogen bonds       : angle       5.91319 ( 1578)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  321 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 310
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
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   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  305 LEU cc_start: 0.8718 (mp) cc_final: 0.8403 (mp)
REVERT: A  388 LEU cc_start: 0.8138 (tp) cc_final: 0.7937 (tt)
REVERT: A  392 ILE cc_start: 0.8155 (mt) cc_final: 0.7754 (tp)
REVERT: C  194 ILE cc_start: 0.8490 (mm) cc_final: 0.8110 (mm)
REVERT: C  413 VAL cc_start: 0.8334 (t) cc_final: 0.8075 (t)
REVERT: D  299 PHE cc_start: 0.8264 (m-80) cc_final: 0.8022 (m-10)
REVERT: D  412 ILE cc_start: 0.8838 (mt) cc_final: 0.8605 (tp)
  outliers start: 11
  outliers final: 9
  residues processed: 316
  average time/residue: 0.2333
  time to fit residues: 96.2599
Evaluate side-chains
  228 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 219
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    9.9990
   chunk 100 optimal weight:    1.9990
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 415 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.124578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.096970 restraints weight = 78644.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.100498 restraints weight = 45297.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.102985 restraints weight = 31386.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.104657 restraints weight = 24149.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.105902 restraints weight = 19969.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.3061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8548  Z= 0.164
  Angle     :  0.564   5.261  11572  Z= 0.325
  Chirality :  0.039   0.149   1364
  Planarity :  0.004   0.035   1408
  Dihedral  :  4.360  18.613   1112
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.27), residues: 1036
  helix:  1.38 (0.19), residues: 752
  sheet:  None (None), residues: 0
  loop : -0.68 (0.40), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 326 
 TYR   0.011   0.002   TYR C 328 
 PHE   0.022   0.002   PHE B 419 
 TRP   0.009   0.001   TRP A 239 
 HIS   0.003   0.001   HIS C 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 8548)
  covalent geometry    : angle       0.56425 (11572)
  hydrogen bonds       : bond        0.05458 (  560)
  hydrogen bonds       : angle       4.92005 ( 1578)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 269
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
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   revert: symmetry clash
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REVERT: B  198 PHE cc_start: 0.8780 (m-80) cc_final: 0.8543 (m-80)
REVERT: B  202 SER cc_start: 0.9357 (t) cc_final: 0.9015 (m)
REVERT: B  243 GLU cc_start: 0.8272 (pp20) cc_final: 0.7982 (pp20)
REVERT: B  356 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8658 (mp0)
REVERT: C  194 ILE cc_start: 0.9762 (mm) cc_final: 0.9335 (mm)
REVERT: C  291 ASN cc_start: 0.8162 (m-40) cc_final: 0.7802 (m-40)
REVERT: D  214 LEU cc_start: 0.9149 (mt) cc_final: 0.8836 (mt)
REVERT: D  299 PHE cc_start: 0.9601 (m-80) cc_final: 0.9176 (m-10)
REVERT: D  353 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8573 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 269
  average time/residue: 0.2304
  time to fit residues: 80.8492
Evaluate side-chains
  214 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 72 optimal weight:    9.9990
   chunk 25 optimal weight:    7.9990
   chunk 63 optimal weight:    5.9990
   chunk 9 optimal weight:   10.0000
   chunk 35 optimal weight:   10.0000
   chunk 31 optimal weight:    8.9990
   chunk 96 optimal weight:   10.0000
   chunk 91 optimal weight:   10.0000
   chunk 101 optimal weight:    0.7980
   chunk 61 optimal weight:    9.9990
   chunk 102 optimal weight:    0.7980
   overall best weight:    4.9186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.123850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.096572 restraints weight = 80238.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.100131 restraints weight = 45875.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.102480 restraints weight = 31606.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.104154 restraints weight = 24376.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.105336 restraints weight = 20128.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.3644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8548  Z= 0.176
  Angle     :  0.542   4.777  11572  Z= 0.312
  Chirality :  0.038   0.148   1364
  Planarity :  0.004   0.031   1408
  Dihedral  :  4.449  19.184   1112
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.27), residues: 1036
  helix:  1.17 (0.19), residues: 770
  sheet:  None (None), residues: 0
  loop : -0.84 (0.41), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 326 
 TYR   0.011   0.001   TYR A 380 
 PHE   0.020   0.002   PHE B 368 
 TRP   0.010   0.001   TRP A 239 
 HIS   0.003   0.001   HIS C 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 8548)
  covalent geometry    : angle       0.54190 (11572)
  hydrogen bonds       : bond        0.04603 (  560)
  hydrogen bonds       : angle       4.86800 ( 1578)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 260
  time to evaluate  : 0.467 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
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   revert: symmetry clash
   revert: symmetry clash
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   revert: symmetry clash
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   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  198 PHE cc_start: 0.8812 (m-80) cc_final: 0.8542 (m-80)
REVERT: B  243 GLU cc_start: 0.8411 (pp20) cc_final: 0.8082 (pp20)
REVERT: C  194 ILE cc_start: 0.9781 (mm) cc_final: 0.9377 (mm)
REVERT: C  300 ARG cc_start: 0.9343 (ptt180) cc_final: 0.8807 (ptm160)
REVERT: D  299 PHE cc_start: 0.9633 (m-80) cc_final: 0.9234 (m-10)
REVERT: D  353 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8427 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 260
  average time/residue: 0.2327
  time to fit residues: 79.1871
Evaluate side-chains
  207 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 33 optimal weight:    9.9990
   chunk 77 optimal weight:    6.9990
   chunk 103 optimal weight:    8.9990
   chunk 46 optimal weight:    8.9990
   chunk 22 optimal weight:    8.9990
   chunk 13 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 93 optimal weight:    8.9990
   chunk 62 optimal weight:    1.9990
   chunk 54 optimal weight:    8.9990
   chunk 9 optimal weight:    9.9990
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 423 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.122302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.094440 restraints weight = 80809.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.097910 restraints weight = 46781.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.100315 restraints weight = 32506.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.101967 restraints weight = 24989.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.103001 restraints weight = 20651.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.4042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8548  Z= 0.222
  Angle     :  0.566   4.626  11572  Z= 0.329
  Chirality :  0.038   0.139   1364
  Planarity :  0.004   0.031   1408
  Dihedral  :  4.566  19.797   1112
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.26), residues: 1036
  helix:  0.91 (0.19), residues: 772
  sheet:  None (None), residues: 0
  loop : -1.02 (0.41), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 300 
 TYR   0.015   0.002   TYR A 380 
 PHE   0.019   0.001   PHE B 368 
 TRP   0.012   0.001   TRP A 239 
 HIS   0.004   0.001   HIS C 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 8548)
  covalent geometry    : angle       0.56572 (11572)
  hydrogen bonds       : bond        0.04281 (  560)
  hydrogen bonds       : angle       4.98423 ( 1578)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
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   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  312 ARG cc_start: 0.8565 (tpp80) cc_final: 0.8335 (mmm-85)
REVERT: B  198 PHE cc_start: 0.8812 (m-80) cc_final: 0.8501 (m-80)
REVERT: B  243 GLU cc_start: 0.8615 (pp20) cc_final: 0.8239 (pp20)
REVERT: C  242 MET cc_start: 0.9212 (ttm) cc_final: 0.8862 (mmt)
REVERT: D  299 PHE cc_start: 0.9664 (m-80) cc_final: 0.9274 (m-10)
REVERT: D  353 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8445 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 245
  average time/residue: 0.2605
  time to fit residues: 82.6769
Evaluate side-chains
  204 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 71 optimal weight:    9.9990
   chunk 89 optimal weight:    8.9990
   chunk 19 optimal weight:   20.0000
   chunk 73 optimal weight:    0.7980
   chunk 72 optimal weight:   10.0000
   chunk 57 optimal weight:    5.9990
   chunk 65 optimal weight:    9.9990
   chunk 75 optimal weight:    9.9990
   chunk 101 optimal weight:    1.9990
   chunk 31 optimal weight:    8.9990
   chunk 96 optimal weight:    0.7980
   overall best weight:    3.7186

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

Flipped N/Q/H residues before XYZ refinement:
D 215 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.111551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.084252 restraints weight = 84627.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.087498 restraints weight = 46483.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.089690 restraints weight = 31135.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.091187 restraints weight = 23529.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.092304 restraints weight = 19387.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.4338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8548  Z= 0.137
  Angle     :  0.517   4.574  11572  Z= 0.292
  Chirality :  0.038   0.160   1364
  Planarity :  0.004   0.031   1408
  Dihedral  :  4.431  19.045   1112
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.27), residues: 1036
  helix:  1.17 (0.19), residues: 771
  sheet:  None (None), residues: 0
  loop : -0.97 (0.40), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 425 
 TYR   0.017   0.002   TYR C 380 
 PHE   0.021   0.001   PHE B 368 
 TRP   0.008   0.001   TRP C 239 
 HIS   0.004   0.001   HIS C 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 8548)
  covalent geometry    : angle       0.51656 (11572)
  hydrogen bonds       : bond        0.04024 (  560)
  hydrogen bonds       : angle       4.62507 ( 1578)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
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   revert: symmetry clash
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   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  310 LEU cc_start: 0.9820 (mm) cc_final: 0.9600 (mm)
REVERT: A  368 PHE cc_start: 0.9234 (m-80) cc_final: 0.8974 (m-10)
REVERT: B  198 PHE cc_start: 0.8809 (m-80) cc_final: 0.8489 (m-80)
REVERT: C  239 TRP cc_start: 0.9402 (t-100) cc_final: 0.9192 (t-100)
REVERT: D  299 PHE cc_start: 0.9654 (m-80) cc_final: 0.9251 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 251
  average time/residue: 0.2365
  time to fit residues: 77.1695
Evaluate side-chains
  205 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 71 optimal weight:    6.9990
   chunk 1 optimal weight:    9.9990
   chunk 102 optimal weight:    0.6980
   chunk 72 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 73 optimal weight:    7.9990
   chunk 32 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 19 optimal weight:    0.3980
   chunk 62 optimal weight:    0.0040
   chunk 44 optimal weight:   10.0000
   overall best weight:    0.5592

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.112804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.085040 restraints weight = 84488.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.088336 restraints weight = 45834.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.090612 restraints weight = 30666.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.092254 restraints weight = 23018.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.093012 restraints weight = 18751.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.4566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   8548  Z= 0.108
  Angle     :  0.498   5.492  11572  Z= 0.276
  Chirality :  0.037   0.163   1364
  Planarity :  0.004   0.044   1408
  Dihedral  :  4.252  18.260   1112
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.27), residues: 1036
  helix:  1.43 (0.19), residues: 778
  sheet:  None (None), residues: 0
  loop : -0.65 (0.42), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 303 
 TYR   0.010   0.001   TYR A 380 
 PHE   0.021   0.001   PHE B 368 
 TRP   0.008   0.001   TRP B 176 
 HIS   0.003   0.001   HIS C 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 8548)
  covalent geometry    : angle       0.49773 (11572)
  hydrogen bonds       : bond        0.03866 (  560)
  hydrogen bonds       : angle       4.27876 ( 1578)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
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   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  310 LEU cc_start: 0.9812 (mm) cc_final: 0.9587 (mm)
REVERT: A  392 ILE cc_start: 0.9582 (mt) cc_final: 0.9219 (tp)
REVERT: A  415 ASN cc_start: 0.9179 (m-40) cc_final: 0.8802 (m110)
REVERT: B  198 PHE cc_start: 0.8810 (m-80) cc_final: 0.8448 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 259
  average time/residue: 0.2418
  time to fit residues: 81.9919
Evaluate side-chains
  210 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 56 optimal weight:    4.9990
   chunk 79 optimal weight:   10.0000
   chunk 59 optimal weight:    0.5980
   chunk 17 optimal weight:    6.9990
   chunk 14 optimal weight:   10.0000
   chunk 7 optimal weight:    9.9990
   chunk 32 optimal weight:    6.9990
   chunk 36 optimal weight:    8.9990
   chunk 76 optimal weight:    2.9990
   chunk 73 optimal weight:    0.0770
   chunk 25 optimal weight:    7.9990
   overall best weight:    3.1344

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

Flipped N/Q/H residues before XYZ refinement:
** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.112554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.085317 restraints weight = 87615.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.088522 restraints weight = 47430.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.090820 restraints weight = 31418.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.092441 restraints weight = 23528.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.093472 restraints weight = 19264.350|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.4774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   8548  Z= 0.128
  Angle     :  0.510   5.828  11572  Z= 0.286
  Chirality :  0.038   0.162   1364
  Planarity :  0.004   0.080   1408
  Dihedral  :  4.266  18.857   1112
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.39 (0.27), residues: 1036
  helix:  1.47 (0.19), residues: 774
  sheet:  None (None), residues: 0
  loop : -0.62 (0.41), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 306 
 TYR   0.014   0.001   TYR A 380 
 PHE   0.018   0.001   PHE B 368 
 TRP   0.010   0.001   TRP A 239 
 HIS   0.002   0.000   HIS C 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 8548)
  covalent geometry    : angle       0.51036 (11572)
  hydrogen bonds       : bond        0.03679 (  560)
  hydrogen bonds       : angle       4.35652 ( 1578)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  312 ARG cc_start: 0.8850 (tpp-160) cc_final: 0.8573 (mmm-85)
REVERT: A  392 ILE cc_start: 0.9584 (mt) cc_final: 0.9246 (tp)
REVERT: A  415 ASN cc_start: 0.9182 (m-40) cc_final: 0.8817 (m110)
REVERT: B  198 PHE cc_start: 0.8773 (m-80) cc_final: 0.8428 (m-80)
REVERT: C  242 MET cc_start: 0.9235 (ttm) cc_final: 0.8885 (mmt)
REVERT: D  300 ARG cc_start: 0.9275 (tpt-90) cc_final: 0.8947 (tpt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 247
  average time/residue: 0.2316
  time to fit residues: 74.9882
Evaluate side-chains
  204 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 83 optimal weight:   10.0000
   chunk 50 optimal weight:    0.6980
   chunk 3 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   chunk 62 optimal weight:    7.9990
   chunk 18 optimal weight:   10.0000
   chunk 103 optimal weight:   10.0000
   chunk 97 optimal weight:    9.9990
   chunk 100 optimal weight:    8.9990
   chunk 56 optimal weight:    0.8980
   overall best weight:    4.5186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.112196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.085068 restraints weight = 87862.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.088222 restraints weight = 47698.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.090477 restraints weight = 31711.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.091880 restraints weight = 23892.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.093043 restraints weight = 19745.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.4906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   8548  Z= 0.155
  Angle     :  0.528   6.429  11572  Z= 0.298
  Chirality :  0.037   0.164   1364
  Planarity :  0.004   0.053   1408
  Dihedral  :  4.286  18.878   1112
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.23 (0.27), residues: 1036
  helix:  1.38 (0.19), residues: 772
  sheet:  None (None), residues: 0
  loop : -0.79 (0.41), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 325 
 TYR   0.019   0.002   TYR B 380 
 PHE   0.019   0.001   PHE A 368 
 TRP   0.013   0.001   TRP A 239 
 HIS   0.002   0.001   HIS C 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8548)
  covalent geometry    : angle       0.52807 (11572)
  hydrogen bonds       : bond        0.03607 (  560)
  hydrogen bonds       : angle       4.42572 ( 1578)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  392 ILE cc_start: 0.9581 (mt) cc_final: 0.9248 (tp)
REVERT: B  198 PHE cc_start: 0.8798 (m-80) cc_final: 0.8447 (m-80)
REVERT: D  199 ILE cc_start: 0.9654 (mm) cc_final: 0.9446 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 238
  average time/residue: 0.2296
  time to fit residues: 71.8552
Evaluate side-chains
  201 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 97 optimal weight:    0.1980
   chunk 9 optimal weight:   10.0000
   chunk 52 optimal weight:   10.0000
   chunk 95 optimal weight:    8.9990
   chunk 96 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 73 optimal weight:    8.9990
   chunk 66 optimal weight:    7.9990
   chunk 56 optimal weight:    6.9990
   chunk 68 optimal weight:    7.9990
   chunk 37 optimal weight:    9.9990
   overall best weight:    3.8388

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

Flipped N/Q/H residues before XYZ refinement:
D 415 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.110787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.084093 restraints weight = 87964.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.087229 restraints weight = 47223.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.089438 restraints weight = 31389.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.090957 restraints weight = 23625.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.092019 restraints weight = 19394.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.5056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8548  Z= 0.139
  Angle     :  0.525   7.161  11572  Z= 0.293
  Chirality :  0.038   0.198   1364
  Planarity :  0.004   0.048   1408
  Dihedral  :  4.250  18.151   1112
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.23 (0.27), residues: 1036
  helix:  1.38 (0.19), residues: 773
  sheet:  None (None), residues: 0
  loop : -0.80 (0.41), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 306 
 TYR   0.018   0.002   TYR B 380 
 PHE   0.020   0.001   PHE A 368 
 TRP   0.012   0.001   TRP A 239 
 HIS   0.002   0.001   HIS C 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 8548)
  covalent geometry    : angle       0.52485 (11572)
  hydrogen bonds       : bond        0.03569 (  560)
  hydrogen bonds       : angle       4.36104 ( 1578)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  368 PHE cc_start: 0.9264 (m-80) cc_final: 0.8986 (m-10)
REVERT: A  392 ILE cc_start: 0.9596 (mt) cc_final: 0.9260 (tp)
REVERT: B  198 PHE cc_start: 0.8818 (m-80) cc_final: 0.8471 (m-80)
REVERT: D  199 ILE cc_start: 0.9645 (mm) cc_final: 0.9445 (mm)
REVERT: D  353 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8544 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 242
  average time/residue: 0.2406
  time to fit residues: 76.0818
Evaluate side-chains
  205 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 91 optimal weight:    3.9990
   chunk 48 optimal weight:    5.9990
   chunk 87 optimal weight:   10.0000
   chunk 15 optimal weight:    8.9990
   chunk 55 optimal weight:    7.9990
   chunk 11 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 31 optimal weight:   10.0000
   chunk 72 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9990
   chunk 5 optimal weight:   20.0000
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.110277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.082921 restraints weight = 86331.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.086135 restraints weight = 47552.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.088332 restraints weight = 31729.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.089825 restraints weight = 24040.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.090809 restraints weight = 19908.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.5212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.114   8548  Z= 0.155
  Angle     :  0.541   7.085  11572  Z= 0.303
  Chirality :  0.038   0.158   1364
  Planarity :  0.004   0.051   1408
  Dihedral  :  4.297  19.665   1112
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.27), residues: 1036
  helix:  1.34 (0.19), residues: 768
  sheet:  None (None), residues: 0
  loop : -0.86 (0.40), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 306 
 TYR   0.015   0.002   TYR A 380 
 PHE   0.020   0.002   PHE A 368 
 TRP   0.013   0.001   TRP A 239 
 HIS   0.002   0.001   HIS C 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 8548)
  covalent geometry    : angle       0.54107 (11572)
  hydrogen bonds       : bond        0.03589 (  560)
  hydrogen bonds       : angle       4.43364 ( 1578)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  368 PHE cc_start: 0.9266 (m-80) cc_final: 0.8989 (m-10)
REVERT: A  392 ILE cc_start: 0.9597 (mt) cc_final: 0.9260 (tp)
REVERT: A  415 ASN cc_start: 0.9244 (m-40) cc_final: 0.8879 (m110)
REVERT: B  198 PHE cc_start: 0.8813 (m-80) cc_final: 0.8459 (m-80)
REVERT: D  299 PHE cc_start: 0.9652 (m-80) cc_final: 0.9238 (m-10)
REVERT: D  300 ARG cc_start: 0.8971 (tpt-90) cc_final: 0.8501 (tpt170)
REVERT: D  353 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8605 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 239
  average time/residue: 0.2407
  time to fit residues: 75.3994
Evaluate side-chains
  200 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 33 optimal weight:   10.0000
   chunk 77 optimal weight:    7.9990
   chunk 38 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 39 optimal weight:    0.9990
   chunk 12 optimal weight:    7.9990
   chunk 92 optimal weight:    0.9980
   chunk 53 optimal weight:    0.3980
   chunk 11 optimal weight:    6.9990
   overall best weight:    2.2786

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

Flipped N/Q/H residues before XYZ refinement:
B 290 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.111004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.083755 restraints weight = 85761.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.086970 restraints weight = 46610.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.089199 restraints weight = 30938.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.090596 restraints weight = 23287.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.091733 restraints weight = 19309.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.5328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8548  Z= 0.120
  Angle     :  0.531   7.763  11572  Z= 0.292
  Chirality :  0.037   0.167   1364
  Planarity :  0.003   0.040   1408
  Dihedral  :  4.239  19.027   1112
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.00 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.30 (0.27), residues: 1036
  helix:  1.41 (0.19), residues: 774
  sheet:  None (None), residues: 0
  loop : -0.67 (0.42), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 306 
 TYR   0.014   0.001   TYR D 380 
 PHE   0.022   0.001   PHE A 368 
 TRP   0.010   0.001   TRP A 239 
 HIS   0.002   0.000   HIS C 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 8548)
  covalent geometry    : angle       0.53128 (11572)
  hydrogen bonds       : bond        0.03559 (  560)
  hydrogen bonds       : angle       4.32019 ( 1578)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2912.14 seconds
wall clock time: 50 minutes 16.18 seconds (3016.18 seconds total)