Starting phenix.real_space_refine
on Mon Jan 13 18:05:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ern_19927/01_2025/9ern_19927.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ern_19927/01_2025/9ern_19927.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ern_19927/01_2025/9ern_19927.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ern_19927/01_2025/9ern_19927.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ern_19927/01_2025/9ern_19927.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ern_19927/01_2025/9ern_19927.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C    2160      2.51       5
     N     636      2.21       5
     O     642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 3444
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 2.70, per 1000 atoms: 0.78
  Number of scatterers: 3444
  At special positions: 0
  Unit cell: (111.24, 136.784, 39.552, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       6     16.00
     O     642      8.00
     N     636      7.00
     C    2160      6.00
    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: 0.75
  Conformation dependent library (CDL) restraints added in 387.6 milliseconds
  

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  792

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 14 sheets defined
      0.0% alpha, 60.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 306 through 310
      removed outlier: 6.532A  pdb=" N   GLN C 307 " --> pdb=" O   ILE D 308 " (cutoff:3.500A)
      removed outlier: 7.904A  pdb=" N   TYR D 310 " --> pdb=" O   GLN C 307 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   VAL C 309 " --> pdb=" O   TYR D 310 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   GLN A 307 " --> pdb=" O   ILE C 308 " (cutoff:3.500A)
      removed outlier: 7.903A  pdb=" N   TYR C 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   VAL A 309 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 313 through 314
      removed outlier: 6.721A  pdb=" N   VAL C 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   VAL A 313 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 317 through 330
      removed outlier: 8.811A  pdb=" N   VAL C 318 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
      removed outlier: 10.768A  pdb=" N   LYS D 321 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
      removed outlier: 9.205A  pdb=" N   SER C 320 " --> pdb=" O   LYS D 321 " (cutoff:3.500A)
      removed outlier: 10.368A  pdb=" N   GLY D 323 " --> pdb=" O   SER C 320 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   CYS C 322 " --> pdb=" O   GLY D 323 " (cutoff:3.500A)
      removed outlier: 7.380A  pdb=" N   LEU D 325 " --> pdb=" O   CYS C 322 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   SER C 324 " --> pdb=" O   LEU D 325 " (cutoff:3.500A)
      removed outlier: 7.900A  pdb=" N   ASN D 327 " --> pdb=" O   SER C 324 " (cutoff:3.500A)
      removed outlier: 9.034A  pdb=" N   GLY C 326 " --> pdb=" O   ASN D 327 " (cutoff:3.500A)
      removed outlier: 8.134A  pdb=" N   HIS D 329 " --> pdb=" O   GLY C 326 " (cutoff:3.500A)
      removed outlier: 9.240A  pdb=" N   ILE C 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
      removed outlier: 8.811A  pdb=" N   VAL A 318 " --> pdb=" O   THR C 319 " (cutoff:3.500A)
      removed outlier: 10.769A  pdb=" N   LYS C 321 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 9.205A  pdb=" N   SER A 320 " --> pdb=" O   LYS C 321 " (cutoff:3.500A)
      removed outlier: 10.368A  pdb=" N   GLY C 323 " --> pdb=" O   SER A 320 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   CYS A 322 " --> pdb=" O   GLY C 323 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   LEU C 325 " --> pdb=" O   CYS A 322 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   SER A 324 " --> pdb=" O   LEU C 325 " (cutoff:3.500A)
      removed outlier: 7.900A  pdb=" N   ASN C 327 " --> pdb=" O   SER A 324 " (cutoff:3.500A)
      removed outlier: 9.034A  pdb=" N   GLY A 326 " --> pdb=" O   ASN C 327 " (cutoff:3.500A)
      removed outlier: 8.134A  pdb=" N   HIS C 329 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 9.239A  pdb=" N   ILE A 328 " --> pdb=" O   HIS C 329 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   VAL E 318 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   THR A 319 " --> pdb=" O   VAL E 318 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   SER E 320 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   LYS A 321 " --> pdb=" O   SER E 320 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   CYS E 322 " --> pdb=" O   LYS A 321 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   GLY A 323 " --> pdb=" O   CYS E 322 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   ILE E 328 " --> pdb=" O   ASN A 327 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   HIS A 329 " --> pdb=" O   ILE E 328 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   HIS E 330 " --> pdb=" O   HIS A 329 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 337 through 346
      removed outlier: 9.063A  pdb=" N   VAL C 337 " --> pdb=" O   GLU D 338 " (cutoff:3.500A)
      removed outlier: 10.291A  pdb=" N   LYS D 340 " --> pdb=" O   VAL C 337 " (cutoff:3.500A)
      removed outlier: 8.968A  pdb=" N   VAL C 339 " --> pdb=" O   LYS D 340 " (cutoff:3.500A)
      removed outlier: 10.293A  pdb=" N   GLU D 342 " --> pdb=" O   VAL C 339 " (cutoff:3.500A)
      removed outlier: 9.073A  pdb=" N   SER C 341 " --> pdb=" O   GLU D 342 " (cutoff:3.500A)
      removed outlier: 9.261A  pdb=" N   LEU D 344 " --> pdb=" O   SER C 341 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   LYS C 343 " --> pdb=" O   LEU D 344 " (cutoff:3.500A)
      removed outlier: 8.181A  pdb=" N   PHE D 346 " --> pdb=" O   LYS C 343 " (cutoff:3.500A)
      removed outlier: 6.185A  pdb=" N   ASP C 345 " --> pdb=" O   PHE D 346 " (cutoff:3.500A)
      removed outlier: 9.063A  pdb=" N   VAL A 337 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
      removed outlier: 10.291A  pdb=" N   LYS C 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 8.968A  pdb=" N   VAL A 339 " --> pdb=" O   LYS C 340 " (cutoff:3.500A)
      removed outlier: 10.292A  pdb=" N   GLU C 342 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 9.073A  pdb=" N   SER A 341 " --> pdb=" O   GLU C 342 " (cutoff:3.500A)
      removed outlier: 9.261A  pdb=" N   LEU C 344 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   LYS A 343 " --> pdb=" O   LEU C 344 " (cutoff:3.500A)
      removed outlier: 8.181A  pdb=" N   PHE C 346 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 6.185A  pdb=" N   ASP A 345 " --> pdb=" O   PHE C 346 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   GLU A 338 " --> pdb=" O   VAL E 337 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   VAL E 339 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   LYS A 340 " --> pdb=" O   VAL E 339 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   SER E 341 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   GLU A 342 " --> pdb=" O   SER E 341 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   LYS E 343 " --> pdb=" O   GLU A 342 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 350 through 357
      removed outlier: 6.567A  pdb=" N   GLN C 351 " --> pdb=" O   SER D 352 " (cutoff:3.500A)
      removed outlier: 8.129A  pdb=" N   ILE D 354 " --> pdb=" O   GLN C 351 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   LYS C 353 " --> pdb=" O   ILE D 354 " (cutoff:3.500A)
      removed outlier: 7.444A  pdb=" N   SER D 356 " --> pdb=" O   LYS C 353 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   GLY C 355 " --> pdb=" O   SER D 356 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   GLN A 351 " --> pdb=" O   SER C 352 " (cutoff:3.500A)
      removed outlier: 8.129A  pdb=" N   ILE C 354 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   LYS A 353 " --> pdb=" O   ILE C 354 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   SER C 356 " --> pdb=" O   LYS A 353 " (cutoff:3.500A)
      removed outlier: 6.120A  pdb=" N   GLY A 355 " --> pdb=" O   SER C 356 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 360 through 362
      removed outlier: 6.376A  pdb=" N   THR A 361 " --> pdb=" O   HIS E 362 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 369 through 378
      removed outlier: 6.358A  pdb=" N   LYS A 370 " --> pdb=" O   ILE E 371 " (cutoff:3.500A)
      removed outlier: 8.131A  pdb=" N   THR E 373 " --> pdb=" O   LYS A 370 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   GLU A 372 " --> pdb=" O   THR E 373 " (cutoff:3.500A)
      removed outlier: 8.333A  pdb=" N   LYS E 375 " --> pdb=" O   GLU A 372 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   HIS A 374 " --> pdb=" O   LYS E 375 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   THR E 377 " --> pdb=" O   HIS A 374 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   LEU A 376 " --> pdb=" O   THR E 377 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 306 through 310
    Processing sheet with id=AA9, first strand: chain 'B' and resid 313 through 314
    Processing sheet with id=AB1, first strand: chain 'B' and resid 317 through 330
      removed outlier: 6.854A  pdb=" N   VAL F 318 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   THR B 319 " --> pdb=" O   VAL F 318 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   SER F 320 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   LYS B 321 " --> pdb=" O   SER F 320 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   CYS F 322 " --> pdb=" O   LYS B 321 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   GLY B 323 " --> pdb=" O   CYS F 322 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   ILE F 328 " --> pdb=" O   ASN B 327 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   HIS B 329 " --> pdb=" O   ILE F 328 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   HIS F 330 " --> pdb=" O   HIS B 329 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 337 through 346
      removed outlier: 6.923A  pdb=" N   GLU B 338 " --> pdb=" O   VAL F 337 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   VAL F 339 " --> pdb=" O   GLU B 338 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   LYS B 340 " --> pdb=" O   VAL F 339 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   SER F 341 " --> pdb=" O   LYS B 340 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   GLU B 342 " --> pdb=" O   SER F 341 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   LYS F 343 " --> pdb=" O   GLU B 342 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 350 through 357
    Processing sheet with id=AB4, first strand: chain 'B' and resid 360 through 362
      removed outlier: 6.376A  pdb=" N   THR B 361 " --> pdb=" O   HIS F 362 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'B' and resid 369 through 378
      removed outlier: 6.358A  pdb=" N   LYS B 370 " --> pdb=" O   ILE F 371 " (cutoff:3.500A)
      removed outlier: 8.131A  pdb=" N   THR F 373 " --> pdb=" O   LYS B 370 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   GLU B 372 " --> pdb=" O   THR F 373 " (cutoff:3.500A)
      removed outlier: 8.333A  pdb=" N   LYS F 375 " --> pdb=" O   GLU B 372 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   HIS B 374 " --> pdb=" O   LYS F 375 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   THR F 377 " --> pdb=" O   HIS B 374 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   LEU B 376 " --> pdb=" O   THR F 377 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5

    60 hydrogen bonds defined for protein.
    180 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: 0.73

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 796
        1.34 -     1.46: 785
        1.46 -     1.58: 1911
        1.58 -     1.70: 0
        1.70 -     1.81: 6
  Bond restraints: 3498
  Sorted by residual:
  bond pdb=" CA  SER F 316 "
       pdb=" CB  SER F 316 "
    ideal  model  delta    sigma   weight residual
    1.529  1.488  0.042 1.64e-02 3.72e+03 6.44e+00
  bond pdb=" CA  SER D 316 "
       pdb=" CB  SER D 316 "
    ideal  model  delta    sigma   weight residual
    1.529  1.488  0.042 1.64e-02 3.72e+03 6.42e+00
  bond pdb=" CA  SER E 316 "
       pdb=" CB  SER E 316 "
    ideal  model  delta    sigma   weight residual
    1.529  1.488  0.042 1.64e-02 3.72e+03 6.42e+00
  bond pdb=" CA  SER A 316 "
       pdb=" CB  SER A 316 "
    ideal  model  delta    sigma   weight residual
    1.529  1.488  0.041 1.64e-02 3.72e+03 6.39e+00
  bond pdb=" CA  SER B 316 "
       pdb=" CB  SER B 316 "
    ideal  model  delta    sigma   weight residual
    1.529  1.488  0.041 1.64e-02 3.72e+03 6.32e+00
  ... (remaining 3493 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.29: 3298
        1.29 -     2.57: 1073
        2.57 -     3.86: 247
        3.86 -     5.15: 50
        5.15 -     6.43: 12
  Bond angle restraints: 4680
  Sorted by residual:
  angle pdb=" N   GLY E 326 "
        pdb=" CA  GLY E 326 "
        pdb=" C   GLY E 326 "
      ideal   model   delta    sigma   weight residual
     110.80  116.87   -6.07 1.41e+00 5.03e-01 1.85e+01
  angle pdb=" N   GLY C 326 "
        pdb=" CA  GLY C 326 "
        pdb=" C   GLY C 326 "
      ideal   model   delta    sigma   weight residual
     110.80  116.85   -6.05 1.41e+00 5.03e-01 1.84e+01
  angle pdb=" N   GLY B 326 "
        pdb=" CA  GLY B 326 "
        pdb=" C   GLY B 326 "
      ideal   model   delta    sigma   weight residual
     110.80  116.85   -6.05 1.41e+00 5.03e-01 1.84e+01
  angle pdb=" N   GLY A 326 "
        pdb=" CA  GLY A 326 "
        pdb=" C   GLY A 326 "
      ideal   model   delta    sigma   weight residual
     110.80  116.85   -6.05 1.41e+00 5.03e-01 1.84e+01
  angle pdb=" N   GLY D 326 "
        pdb=" CA  GLY D 326 "
        pdb=" C   GLY D 326 "
      ideal   model   delta    sigma   weight residual
     110.80  116.84   -6.04 1.41e+00 5.03e-01 1.84e+01
  ... (remaining 4675 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.49: 1824
       11.49 -    22.98: 240
       22.98 -    34.47: 42
       34.47 -    45.95: 18
       45.95 -    57.44: 12
  Dihedral angle restraints: 2136
    sinusoidal: 894
      harmonic: 1242
  Sorted by residual:
  dihedral pdb=" CA  VAL C 318 "
           pdb=" C   VAL C 318 "
           pdb=" N   THR C 319 "
           pdb=" CA  THR C 319 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.03  -24.97     0      5.00e+00 4.00e-02 2.49e+01
  dihedral pdb=" CA  VAL B 318 "
           pdb=" C   VAL B 318 "
           pdb=" N   THR B 319 "
           pdb=" CA  THR B 319 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.03  -24.97     0      5.00e+00 4.00e-02 2.49e+01
  dihedral pdb=" CA  VAL D 318 "
           pdb=" C   VAL D 318 "
           pdb=" N   THR D 319 "
           pdb=" CA  THR D 319 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.06  -24.94     0      5.00e+00 4.00e-02 2.49e+01
  ... (remaining 2133 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.047: 186
       0.047 -    0.092: 211
       0.092 -    0.137: 101
       0.137 -    0.182: 16
       0.182 -    0.226: 14
  Chirality restraints: 528
  Sorted by residual:
  chirality pdb=" CB  ILE F 328 "
            pdb=" CA  ILE F 328 "
            pdb=" CG1 ILE F 328 "
            pdb=" CG2 ILE F 328 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CB  ILE E 328 "
            pdb=" CA  ILE E 328 "
            pdb=" CG1 ILE E 328 "
            pdb=" CG2 ILE E 328 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CB  ILE B 328 "
            pdb=" CA  ILE B 328 "
            pdb=" CG1 ILE B 328 "
            pdb=" CG2 ILE B 328 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.27e+00
  ... (remaining 525 not shown)

  Planarity restraints: 594
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 310 "   -0.029 2.00e-02 2.50e+03   1.70e-02 5.75e+00
        pdb=" CG  TYR C 310 "    0.036 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 310 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 310 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 310 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 310 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 310 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR C 310 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F 310 "    0.029 2.00e-02 2.50e+03   1.68e-02 5.65e+00
        pdb=" CG  TYR F 310 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 TYR F 310 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR F 310 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR F 310 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR F 310 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR F 310 "    0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR F 310 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 310 "   -0.029 2.00e-02 2.50e+03   1.68e-02 5.65e+00
        pdb=" CG  TYR E 310 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 310 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 310 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 310 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 310 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 310 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR E 310 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 591 not shown)

  Histogram of nonbonded interaction distances:
        2.54 -     3.01: 1736
        3.01 -     3.48: 2843
        3.48 -     3.96: 5484
        3.96 -     4.43: 5487
        4.43 -     4.90: 10434
  Nonbonded interactions: 25984
  Sorted by model distance:
  nonbonded pdb=" OG  SER F 316 "
            pdb=" NZ  LYS F 370 "
     model   vdw
     2.539 3.120
  nonbonded pdb=" OG  SER C 316 "
            pdb=" NZ  LYS C 370 "
     model   vdw
     2.540 3.120
  nonbonded pdb=" OG  SER E 316 "
            pdb=" NZ  LYS E 370 "
     model   vdw
     2.540 3.120
  nonbonded pdb=" OG  SER A 316 "
            pdb=" NZ  LYS A 370 "
     model   vdw
     2.540 3.120
  nonbonded pdb=" OG  SER B 316 "
            pdb=" NZ  LYS B 370 "
     model   vdw
     2.540 3.120
  ... (remaining 25979 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.780
  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:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.510
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8884
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      :  0.009   0.054   3498  Z= 0.606
  Angle     :  1.379   6.432   4680  Z= 0.910
  Chirality :  0.082   0.226    528
  Planarity :  0.008   0.034    594
  Dihedral  : 11.585  57.442   1344
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  :  3.03 %
    Favored  : 93.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.81 (0.30), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.13 (0.23), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.012   0.004   HIS B 329 
 PHE   0.026   0.006   PHE E 346 
 TYR   0.036   0.011   TYR B 310 
 ARG   0.001   0.000   ARG E 379 

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 136
  time to evaluate  : 0.445 
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: A  340 LYS cc_start: 0.8547 (mtpm) cc_final: 0.8171 (mttp)
REVERT: A  345 ASP cc_start: 0.9016 (m-30) cc_final: 0.8507 (t0)
REVERT: B  338 GLU cc_start: 0.8830 (tt0) cc_final: 0.8604 (tt0)
REVERT: B  340 LYS cc_start: 0.8677 (mtpm) cc_final: 0.8296 (mttp)
REVERT: C  340 LYS cc_start: 0.8596 (mtpm) cc_final: 0.8216 (mttt)
REVERT: C  373 THR cc_start: 0.8702 (m) cc_final: 0.8133 (p)
REVERT: D  317 LYS cc_start: 0.8616 (pttt) cc_final: 0.8393 (ptpt)
REVERT: D  340 LYS cc_start: 0.8786 (mtpm) cc_final: 0.8429 (mttt)
REVERT: D  373 THR cc_start: 0.8887 (m) cc_final: 0.8472 (p)
REVERT: E  340 LYS cc_start: 0.8609 (mtpm) cc_final: 0.8233 (mttp)
REVERT: E  348 ASP cc_start: 0.8979 (t0) cc_final: 0.8722 (t0)
REVERT: E  349 ARG cc_start: 0.9067 (mtt180) cc_final: 0.7437 (tpt90)
REVERT: F  340 LYS cc_start: 0.8596 (mtpm) cc_final: 0.8206 (mttt)
REVERT: F  349 ARG cc_start: 0.9046 (mtt180) cc_final: 0.7331 (tpt90)
  outliers start: 12
  outliers final: 0
  residues processed: 142
  average time/residue: 1.4691
  time to fit residues: 213.2542
Evaluate side-chains
  113 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 10 optimal weight:    9.9990
   chunk 21 optimal weight:   10.0000
   chunk 32 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 20 optimal weight:    9.9990
   chunk 24 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 11 optimal weight:    0.3980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 330 HIS
A 336 GLN
A 362 HIS
B 327 ASN
B 330 HIS
C 330 HIS
C 336 GLN
C 351 GLN
C 362 HIS
D 330 HIS
D 362 HIS
E 327 ASN
E 336 GLN
E 351 GLN
E 362 HIS
F 330 HIS
F 351 GLN
F 362 HIS

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.161241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.119570 restraints weight = 3532.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3754 rms_B_bonded: 1.79
r_work: 0.3639 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3547 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8739
moved from start:          0.2184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   3498  Z= 0.151
  Angle     :  0.538   3.817   4680  Z= 0.285
  Chirality :  0.049   0.136    528
  Planarity :  0.004   0.034    594
  Dihedral  :  4.993  15.377    462
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 14.65 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.14 (0.32), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.62 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 329 
 PHE   0.008   0.001   PHE A 346 
 TYR   0.015   0.003   TYR B 310 
 ARG   0.001   0.000   ARG D 379 

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 140
  time to evaluate  : 0.410 
Fit side-chains
REVERT: A  340 LYS cc_start: 0.8410 (mtpm) cc_final: 0.8102 (mttt)
REVERT: A  375 LYS cc_start: 0.8029 (tttt) cc_final: 0.7669 (tttm)
REVERT: B  311 LYS cc_start: 0.8425 (mtmt) cc_final: 0.6777 (pptt)
REVERT: B  338 GLU cc_start: 0.8561 (tt0) cc_final: 0.8324 (tt0)
REVERT: B  340 LYS cc_start: 0.8636 (mtpm) cc_final: 0.8255 (mttt)
REVERT: B  347 LYS cc_start: 0.8883 (mptt) cc_final: 0.8652 (mptp)
REVERT: C  340 LYS cc_start: 0.8436 (mtpm) cc_final: 0.8031 (mttt)
REVERT: C  345 ASP cc_start: 0.8393 (m-30) cc_final: 0.8009 (t0)
REVERT: C  375 LYS cc_start: 0.8215 (tttt) cc_final: 0.7853 (tttm)
REVERT: D  311 LYS cc_start: 0.8365 (mtmt) cc_final: 0.6756 (pptt)
REVERT: D  317 LYS cc_start: 0.8537 (pttt) cc_final: 0.8275 (ptpt)
REVERT: D  321 LYS cc_start: 0.8581 (ttpt) cc_final: 0.8331 (mtmm)
REVERT: D  340 LYS cc_start: 0.8610 (mtpm) cc_final: 0.8261 (mttt)
REVERT: D  373 THR cc_start: 0.8639 (m) cc_final: 0.8437 (p)
REVERT: D  375 LYS cc_start: 0.8681 (tttt) cc_final: 0.8476 (tttt)
REVERT: E  311 LYS cc_start: 0.7939 (mtmt) cc_final: 0.7479 (mmtt)
REVERT: E  340 LYS cc_start: 0.8416 (mtpm) cc_final: 0.8055 (mttt)
REVERT: E  349 ARG cc_start: 0.8726 (mtt180) cc_final: 0.7288 (mmp-170)
REVERT: E  375 LYS cc_start: 0.8124 (tttt) cc_final: 0.7691 (tttm)
REVERT: F  311 LYS cc_start: 0.7903 (mtmt) cc_final: 0.7442 (mmtt)
REVERT: F  340 LYS cc_start: 0.8424 (mtpm) cc_final: 0.7970 (mttt)
REVERT: F  347 LYS cc_start: 0.8768 (mptt) cc_final: 0.8521 (mptp)
REVERT: F  349 ARG cc_start: 0.8723 (mtt180) cc_final: 0.7123 (mmp-170)
REVERT: F  373 THR cc_start: 0.8402 (m) cc_final: 0.7897 (p)
REVERT: F  375 LYS cc_start: 0.8059 (tttt) cc_final: 0.7723 (tttt)
  outliers start: 7
  outliers final: 1
  residues processed: 143
  average time/residue: 1.4247
  time to fit residues: 208.4167
Evaluate side-chains
  120 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 119
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  320 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:    7.9990
   chunk 34 optimal weight:    1.9990
   chunk 7 optimal weight:   10.0000
   chunk 24 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   chunk 27 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   chunk 3 optimal weight:    7.9990
   chunk 16 optimal weight:   10.0000
   chunk 25 optimal weight:    0.8980
   overall best weight:    3.3788

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

Flipped N/Q/H residues before XYZ refinement:
B 362 HIS
E 330 HIS
E 351 GLN
E 368 ASN
F 351 GLN
F 368 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.155516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.113339 restraints weight = 3543.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3685 rms_B_bonded: 1.81
r_work: 0.3569 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3479 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8796
moved from start:          0.2494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   3498  Z= 0.318
  Angle     :  0.616   4.275   4680  Z= 0.321
  Chirality :  0.051   0.131    528
  Planarity :  0.004   0.027    594
  Dihedral  :  4.995  15.733    462
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.44 %
    Favored  : 78.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.96 (0.33), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.48 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 329 
 PHE   0.011   0.002   PHE A 346 
 TYR   0.015   0.004   TYR B 310 
 ARG   0.001   0.000   ARG F 349 

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 127
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.8393 (mtpm) cc_final: 0.8065 (mttt)
REVERT: A  375 LYS cc_start: 0.8030 (tttt) cc_final: 0.7585 (tttm)
REVERT: B  311 LYS cc_start: 0.8457 (mtmt) cc_final: 0.7117 (pptt)
REVERT: B  317 LYS cc_start: 0.8675 (ptpt) cc_final: 0.8470 (ptpt)
REVERT: B  338 GLU cc_start: 0.8548 (tt0) cc_final: 0.8239 (tt0)
REVERT: B  340 LYS cc_start: 0.8693 (mtpm) cc_final: 0.8240 (mttt)
REVERT: B  375 LYS cc_start: 0.8441 (tttm) cc_final: 0.7890 (tppp)
REVERT: C  340 LYS cc_start: 0.8411 (mtpm) cc_final: 0.7990 (mttt)
REVERT: C  373 THR cc_start: 0.8446 (m) cc_final: 0.8023 (p)
REVERT: C  375 LYS cc_start: 0.8304 (tttt) cc_final: 0.7952 (tttm)
REVERT: D  311 LYS cc_start: 0.8394 (mtmt) cc_final: 0.7103 (pptt)
REVERT: D  317 LYS cc_start: 0.8595 (pttt) cc_final: 0.8320 (ptpt)
REVERT: D  340 LYS cc_start: 0.8561 (mtpm) cc_final: 0.8210 (mttt)
REVERT: D  373 THR cc_start: 0.8677 (m) cc_final: 0.8390 (p)
REVERT: E  311 LYS cc_start: 0.8158 (mtmt) cc_final: 0.7718 (mmtt)
REVERT: E  340 LYS cc_start: 0.8422 (mtpm) cc_final: 0.8034 (mttt)
REVERT: E  349 ARG cc_start: 0.8726 (mtt180) cc_final: 0.7295 (mtp180)
REVERT: E  375 LYS cc_start: 0.8157 (tttt) cc_final: 0.7732 (tttm)
REVERT: F  311 LYS cc_start: 0.8069 (mtmt) cc_final: 0.7599 (mmtt)
REVERT: F  331 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8810 (ttmt)
REVERT: F  340 LYS cc_start: 0.8411 (mtpm) cc_final: 0.7977 (mttt)
REVERT: F  347 LYS cc_start: 0.8804 (mptt) cc_final: 0.8542 (mptp)
REVERT: F  373 THR cc_start: 0.8457 (m) cc_final: 0.8061 (p)
REVERT: F  375 LYS cc_start: 0.8084 (tttt) cc_final: 0.7756 (tttt)
  outliers start: 9
  outliers final: 5
  residues processed: 132
  average time/residue: 1.4746
  time to fit residues: 198.9778
Evaluate side-chains
  127 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 121
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain F residue  331 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:    8.9990
   chunk 13 optimal weight:    0.3980
   chunk 7 optimal weight:   10.0000
   chunk 33 optimal weight:    4.9990
   chunk 29 optimal weight:   10.0000
   chunk 22 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 21 optimal weight:    8.9990
   chunk 14 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    3.2788

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

Flipped N/Q/H residues before XYZ refinement:
F 351 GLN
F 368 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.154830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.112850 restraints weight = 3599.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 1.82
r_work: 0.3558 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3468 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8800
moved from start:          0.2763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3498  Z= 0.307
  Angle     :  0.597   4.444   4680  Z= 0.309
  Chirality :  0.050   0.131    528
  Planarity :  0.003   0.021    594
  Dihedral  :  4.946  15.659    462
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 21.21 %
    Favored  : 76.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.88 (0.33), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.42 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 329 
 PHE   0.009   0.002   PHE A 346 
 TYR   0.014   0.004   TYR B 310 
 ARG   0.001   0.000   ARG F 349 

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 122
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.8384 (mtpm) cc_final: 0.8065 (mttt)
REVERT: A  375 LYS cc_start: 0.7979 (tttt) cc_final: 0.7556 (tttm)
REVERT: B  311 LYS cc_start: 0.8424 (mtmt) cc_final: 0.7218 (pptt)
REVERT: B  338 GLU cc_start: 0.8555 (tt0) cc_final: 0.8308 (tt0)
REVERT: B  340 LYS cc_start: 0.8693 (mtpm) cc_final: 0.8230 (mttt)
REVERT: B  375 LYS cc_start: 0.8363 (tttm) cc_final: 0.7880 (tppp)
REVERT: C  340 LYS cc_start: 0.8440 (mtpm) cc_final: 0.7986 (mttt)
REVERT: C  373 THR cc_start: 0.8460 (m) cc_final: 0.8034 (p)
REVERT: C  375 LYS cc_start: 0.8296 (tttt) cc_final: 0.7962 (tttm)
REVERT: D  311 LYS cc_start: 0.8408 (mtmt) cc_final: 0.7177 (pptt)
REVERT: D  340 LYS cc_start: 0.8544 (mtpm) cc_final: 0.8189 (mttt)
REVERT: D  373 THR cc_start: 0.8676 (m) cc_final: 0.8390 (p)
REVERT: E  311 LYS cc_start: 0.8173 (mtmt) cc_final: 0.7801 (mmtt)
REVERT: E  317 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8152 (ptpp)
REVERT: E  340 LYS cc_start: 0.8409 (mtpm) cc_final: 0.8037 (mttt)
REVERT: E  349 ARG cc_start: 0.8753 (mtt180) cc_final: 0.7286 (mtp180)
REVERT: E  375 LYS cc_start: 0.8159 (tttt) cc_final: 0.7738 (tttm)
REVERT: F  311 LYS cc_start: 0.8008 (mtmt) cc_final: 0.7577 (mmtt)
REVERT: F  331 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8826 (ttmt)
REVERT: F  340 LYS cc_start: 0.8390 (mtpm) cc_final: 0.7961 (mttt)
REVERT: F  347 LYS cc_start: 0.8783 (mptt) cc_final: 0.8518 (mptp)
REVERT: F  349 ARG cc_start: 0.8734 (mtt180) cc_final: 0.6988 (tpt90)
REVERT: F  373 THR cc_start: 0.8487 (m) cc_final: 0.8121 (p)
REVERT: F  375 LYS cc_start: 0.8053 (tttt) cc_final: 0.7846 (tttm)
  outliers start: 10
  outliers final: 2
  residues processed: 126
  average time/residue: 1.3763
  time to fit residues: 177.4878
Evaluate side-chains
  125 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 121
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain E residue  317 LYS
Chi-restraints excluded: chain F residue  331 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 7 optimal weight:   10.0000
   chunk 15 optimal weight:   10.0000
   chunk 30 optimal weight:    6.9990
   chunk 25 optimal weight:    0.7980
   chunk 6 optimal weight:    9.9990
   chunk 22 optimal weight:    7.9990
   chunk 3 optimal weight:    7.9990
   chunk 32 optimal weight:    6.9990
   chunk 1 optimal weight:   10.0000
   overall best weight:    5.1588

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

Flipped N/Q/H residues before XYZ refinement:
F 351 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.151975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.110054 restraints weight = 3618.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 1.82
r_work: 0.3525 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3435 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8832
moved from start:          0.2839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.051   3498  Z= 0.465
  Angle     :  0.689   6.136   4680  Z= 0.356
  Chirality :  0.053   0.138    528
  Planarity :  0.003   0.015    594
  Dihedral  :  5.203  16.332    462
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 21.46 %
    Favored  : 75.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.84 (0.34), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.39 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 329 
 PHE   0.011   0.002   PHE A 346 
 TYR   0.015   0.004   TYR C 310 
 ARG   0.001   0.000   ARG F 349 

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 124
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8609 (mtmt)
REVERT: A  340 LYS cc_start: 0.8457 (mtpm) cc_final: 0.8014 (mttp)
REVERT: A  375 LYS cc_start: 0.8018 (tttt) cc_final: 0.7641 (tttm)
REVERT: B  311 LYS cc_start: 0.8458 (mtmt) cc_final: 0.7398 (pptt)
REVERT: B  340 LYS cc_start: 0.8683 (mtpm) cc_final: 0.8245 (mttt)
REVERT: B  373 THR cc_start: 0.8820 (m) cc_final: 0.8559 (p)
REVERT: C  340 LYS cc_start: 0.8461 (mtpm) cc_final: 0.8015 (mtmt)
REVERT: C  373 THR cc_start: 0.8491 (m) cc_final: 0.8108 (p)
REVERT: C  375 LYS cc_start: 0.8300 (tttt) cc_final: 0.7977 (tttm)
REVERT: D  311 LYS cc_start: 0.8488 (mtmt) cc_final: 0.7279 (pptt)
REVERT: D  340 LYS cc_start: 0.8539 (mtpm) cc_final: 0.8201 (mttt)
REVERT: D  373 THR cc_start: 0.8682 (m) cc_final: 0.8395 (p)
REVERT: E  311 LYS cc_start: 0.8273 (mtmt) cc_final: 0.7888 (mmtt)
REVERT: E  317 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8061 (ptpp)
REVERT: E  331 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8735 (mtmm)
REVERT: E  340 LYS cc_start: 0.8403 (mtpm) cc_final: 0.8043 (mttt)
REVERT: E  349 ARG cc_start: 0.8767 (mtt180) cc_final: 0.7355 (mtp180)
REVERT: E  375 LYS cc_start: 0.8203 (tttt) cc_final: 0.7785 (tttm)
REVERT: F  311 LYS cc_start: 0.8134 (mtmt) cc_final: 0.7669 (mmtt)
REVERT: F  331 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8894 (ttmt)
REVERT: F  340 LYS cc_start: 0.8398 (mtpm) cc_final: 0.8013 (mttt)
REVERT: F  347 LYS cc_start: 0.8824 (mptt) cc_final: 0.8605 (mptp)
REVERT: F  349 ARG cc_start: 0.8767 (mtt180) cc_final: 0.7022 (tpt90)
  outliers start: 11
  outliers final: 3
  residues processed: 131
  average time/residue: 1.4213
  time to fit residues: 190.3128
Evaluate side-chains
  132 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 125
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  331 LYS
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain E residue  317 LYS
Chi-restraints excluded: chain E residue  331 LYS
Chi-restraints excluded: chain F residue  331 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 24 optimal weight:    7.9990
   chunk 6 optimal weight:   10.0000
   chunk 21 optimal weight:    4.9990
   chunk 7 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 2 optimal weight:    0.8980
   chunk 15 optimal weight:    9.9990
   chunk 40 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   overall best weight:    2.7786

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

Flipped N/Q/H residues before XYZ refinement:
F 351 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.154866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.112899 restraints weight = 3658.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 1.81
r_work: 0.3568 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3480 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8805
moved from start:          0.2981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3498  Z= 0.262
  Angle     :  0.571   4.529   4680  Z= 0.293
  Chirality :  0.050   0.129    528
  Planarity :  0.002   0.013    594
  Dihedral  :  4.914  15.284    462
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 21.21 %
    Favored  : 75.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.75 (0.34), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.33 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 329 
 PHE   0.008   0.001   PHE A 346 
 TYR   0.012   0.003   TYR A 310 
 ARG   0.001   0.000   ARG B 379 

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8410 (mtmt)
REVERT: A  340 LYS cc_start: 0.8366 (mtpm) cc_final: 0.8029 (mttt)
REVERT: A  375 LYS cc_start: 0.7957 (tttt) cc_final: 0.7711 (tptm)
REVERT: B  311 LYS cc_start: 0.8414 (mtmt) cc_final: 0.7336 (pptt)
REVERT: B  338 GLU cc_start: 0.8535 (tt0) cc_final: 0.8043 (tt0)
REVERT: B  340 LYS cc_start: 0.8674 (mtpm) cc_final: 0.8245 (mtmt)
REVERT: B  373 THR cc_start: 0.8783 (m) cc_final: 0.8529 (p)
REVERT: B  375 LYS cc_start: 0.8326 (tttm) cc_final: 0.7874 (tppp)
REVERT: C  340 LYS cc_start: 0.8395 (mtpm) cc_final: 0.7986 (mtmt)
REVERT: C  373 THR cc_start: 0.8480 (m) cc_final: 0.8066 (p)
REVERT: C  375 LYS cc_start: 0.8253 (tttt) cc_final: 0.7935 (tttm)
REVERT: D  311 LYS cc_start: 0.8437 (mtmt) cc_final: 0.7292 (pptt)
REVERT: D  340 LYS cc_start: 0.8501 (mtpm) cc_final: 0.8160 (mttt)
REVERT: D  373 THR cc_start: 0.8624 (m) cc_final: 0.8372 (p)
REVERT: E  311 LYS cc_start: 0.8214 (mtmt) cc_final: 0.7805 (mmtt)
REVERT: E  317 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8128 (ptpp)
REVERT: E  331 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8714 (mtmm)
REVERT: E  340 LYS cc_start: 0.8375 (mtpm) cc_final: 0.8046 (mttt)
REVERT: E  349 ARG cc_start: 0.8734 (mtt180) cc_final: 0.7301 (mmp-170)
REVERT: E  375 LYS cc_start: 0.8174 (tttt) cc_final: 0.7764 (tttm)
REVERT: F  311 LYS cc_start: 0.8094 (mtmt) cc_final: 0.7632 (mmtt)
REVERT: F  340 LYS cc_start: 0.8378 (mtpm) cc_final: 0.8000 (mttt)
REVERT: F  347 LYS cc_start: 0.8839 (mptt) cc_final: 0.8613 (mptp)
REVERT: F  349 ARG cc_start: 0.8759 (mtt180) cc_final: 0.7025 (tpt90)
  outliers start: 13
  outliers final: 2
  residues processed: 128
  average time/residue: 1.4140
  time to fit residues: 185.1507
Evaluate side-chains
  120 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 115
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 LYS
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain E residue  317 LYS
Chi-restraints excluded: chain E residue  331 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    9.9990
   chunk 15 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 16 optimal weight:    8.9990
   chunk 2 optimal weight:    2.9990
   chunk 9 optimal weight:    6.9990
   chunk 20 optimal weight:    5.9990
   chunk 3 optimal weight:    8.9990
   chunk 37 optimal weight:    2.9990
   chunk 24 optimal weight:    7.9990
   chunk 39 optimal weight:    6.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
F 351 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.152266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.110240 restraints weight = 3651.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 1.82
r_work: 0.3531 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3442 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8830
moved from start:          0.3000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049   3498  Z= 0.448
  Angle     :  0.678   6.284   4680  Z= 0.348
  Chirality :  0.052   0.137    528
  Planarity :  0.003   0.017    594
  Dihedral  :  5.195  16.538    462
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 22.22 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.34), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.34 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 329 
 PHE   0.011   0.002   PHE A 346 
 TYR   0.015   0.004   TYR C 310 
 ARG   0.002   0.000   ARG B 379 

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8616 (mtmt)
REVERT: A  340 LYS cc_start: 0.8449 (mtpm) cc_final: 0.8008 (mttp)
REVERT: A  373 THR cc_start: 0.8444 (m) cc_final: 0.7949 (p)
REVERT: A  375 LYS cc_start: 0.7996 (tttt) cc_final: 0.7616 (tttm)
REVERT: B  311 LYS cc_start: 0.8455 (mtmt) cc_final: 0.7405 (pptt)
REVERT: B  340 LYS cc_start: 0.8666 (mtpm) cc_final: 0.8258 (mttt)
REVERT: B  373 THR cc_start: 0.8789 (m) cc_final: 0.8532 (p)
REVERT: C  340 LYS cc_start: 0.8447 (mtpm) cc_final: 0.8009 (mtmt)
REVERT: C  373 THR cc_start: 0.8498 (m) cc_final: 0.8045 (p)
REVERT: C  375 LYS cc_start: 0.8291 (tttt) cc_final: 0.7978 (tttm)
REVERT: D  311 LYS cc_start: 0.8494 (mtmt) cc_final: 0.7322 (pptt)
REVERT: D  314 ASP cc_start: 0.8520 (t0) cc_final: 0.8175 (t0)
REVERT: D  340 LYS cc_start: 0.8539 (mtpm) cc_final: 0.8191 (mttt)
REVERT: D  373 THR cc_start: 0.8675 (m) cc_final: 0.8398 (p)
REVERT: E  311 LYS cc_start: 0.8279 (mtmt) cc_final: 0.7877 (mmtt)
REVERT: E  317 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8105 (ptpp)
REVERT: E  331 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8726 (mtmm)
REVERT: E  340 LYS cc_start: 0.8380 (mtpm) cc_final: 0.8034 (mttt)
REVERT: E  349 ARG cc_start: 0.8785 (mtt180) cc_final: 0.7358 (mtp180)
REVERT: E  375 LYS cc_start: 0.8176 (tttt) cc_final: 0.7773 (tttm)
REVERT: F  311 LYS cc_start: 0.8148 (mtmt) cc_final: 0.7676 (mmtt)
REVERT: F  340 LYS cc_start: 0.8415 (mtpm) cc_final: 0.8021 (mttt)
REVERT: F  347 LYS cc_start: 0.8848 (mptt) cc_final: 0.8641 (mptp)
REVERT: F  349 ARG cc_start: 0.8767 (mtt180) cc_final: 0.7029 (tpt90)
REVERT: F  375 LYS cc_start: 0.8060 (tttm) cc_final: 0.7658 (tttp)
  outliers start: 11
  outliers final: 3
  residues processed: 124
  average time/residue: 1.3566
  time to fit residues: 172.2708
Evaluate side-chains
  124 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 118
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 LYS
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain E residue  317 LYS
Chi-restraints excluded: chain E residue  331 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 31 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0060
   chunk 18 optimal weight:    0.8980
   chunk 25 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   chunk 41 optimal weight:    4.9990
   overall best weight:    1.9802

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.155785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.113805 restraints weight = 3634.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 1.82
r_work: 0.3583 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3493 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8796
moved from start:          0.3140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3498  Z= 0.201
  Angle     :  0.558   9.181   4680  Z= 0.279
  Chirality :  0.050   0.174    528
  Planarity :  0.002   0.014    594
  Dihedral  :  4.808  15.205    462
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 23.23 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.69 (0.34), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.28 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS E 329 
 PHE   0.008   0.001   PHE A 346 
 TYR   0.011   0.003   TYR B 310 
 ARG   0.001   0.000   ARG B 379 

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 117
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.8338 (mtpm) cc_final: 0.8053 (mttt)
REVERT: A  375 LYS cc_start: 0.7926 (tttt) cc_final: 0.7677 (tptm)
REVERT: B  311 LYS cc_start: 0.8420 (mtmt) cc_final: 0.7366 (pptt)
REVERT: B  338 GLU cc_start: 0.8535 (tt0) cc_final: 0.8287 (tt0)
REVERT: B  340 LYS cc_start: 0.8670 (mtpm) cc_final: 0.8242 (mtmt)
REVERT: B  375 LYS cc_start: 0.8304 (tttm) cc_final: 0.7845 (tppp)
REVERT: C  340 LYS cc_start: 0.8379 (mtpm) cc_final: 0.7972 (mtmt)
REVERT: C  373 THR cc_start: 0.8488 (m) cc_final: 0.8074 (p)
REVERT: C  375 LYS cc_start: 0.8220 (tttt) cc_final: 0.7918 (tttm)
REVERT: D  311 LYS cc_start: 0.8437 (mtmt) cc_final: 0.7315 (pptt)
REVERT: D  314 ASP cc_start: 0.8421 (t0) cc_final: 0.8112 (t0)
REVERT: D  340 LYS cc_start: 0.8482 (mtpm) cc_final: 0.8136 (mttt)
REVERT: D  373 THR cc_start: 0.8581 (m) cc_final: 0.8362 (p)
REVERT: E  311 LYS cc_start: 0.8177 (mtmt) cc_final: 0.7821 (mmtt)
REVERT: E  331 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8728 (mtmm)
REVERT: E  340 LYS cc_start: 0.8343 (mtpm) cc_final: 0.8014 (mttp)
REVERT: E  349 ARG cc_start: 0.8743 (mtt180) cc_final: 0.7307 (mmp-170)
REVERT: E  375 LYS cc_start: 0.8146 (tttt) cc_final: 0.7752 (tttm)
REVERT: F  311 LYS cc_start: 0.8083 (mtmt) cc_final: 0.7643 (mmtt)
REVERT: F  340 LYS cc_start: 0.8370 (mtpm) cc_final: 0.7984 (mttt)
REVERT: F  347 LYS cc_start: 0.8837 (mptt) cc_final: 0.8627 (mptp)
  outliers start: 7
  outliers final: 3
  residues processed: 121
  average time/residue: 1.3648
  time to fit residues: 169.0999
Evaluate side-chains
  121 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 117
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain E residue  331 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 8 optimal weight:    8.9990
   chunk 27 optimal weight:    6.9990
   chunk 37 optimal weight:    0.6980
   chunk 39 optimal weight:    7.9990
   chunk 17 optimal weight:    0.7980
   chunk 14 optimal weight:    5.9990
   chunk 13 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 21 optimal weight:    7.9990
   overall best weight:    1.4182

-------------------------------------------------------------------------------
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 = 0.4212 r_free = 0.4212 target = 0.157150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.115210 restraints weight = 3571.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 1.80
r_work: 0.3606 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3520 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8776
moved from start:          0.3260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3498  Z= 0.159
  Angle     :  0.528   9.756   4680  Z= 0.260
  Chirality :  0.049   0.129    528
  Planarity :  0.002   0.014    594
  Dihedral  :  4.551  14.272    462
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 23.48 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.34), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.21 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS E 329 
 PHE   0.008   0.001   PHE A 346 
 TYR   0.010   0.002   TYR B 310 
 ARG   0.001   0.000   ARG D 379 

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 121
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8469 (mtmt)
REVERT: A  340 LYS cc_start: 0.8336 (mtpm) cc_final: 0.8044 (mttt)
REVERT: A  375 LYS cc_start: 0.7913 (tttt) cc_final: 0.7666 (tptm)
REVERT: B  311 LYS cc_start: 0.8414 (mtmt) cc_final: 0.7381 (pptt)
REVERT: B  338 GLU cc_start: 0.8526 (tt0) cc_final: 0.8130 (tt0)
REVERT: B  340 LYS cc_start: 0.8630 (mtpm) cc_final: 0.8217 (mtmt)
REVERT: B  375 LYS cc_start: 0.8272 (tttm) cc_final: 0.7824 (tppp)
REVERT: C  340 LYS cc_start: 0.8350 (mtpm) cc_final: 0.7941 (mtmt)
REVERT: C  373 THR cc_start: 0.8460 (m) cc_final: 0.8023 (p)
REVERT: C  375 LYS cc_start: 0.8154 (tttt) cc_final: 0.7848 (tttm)
REVERT: D  311 LYS cc_start: 0.8463 (mtmt) cc_final: 0.7339 (pptt)
REVERT: D  314 ASP cc_start: 0.8366 (t0) cc_final: 0.8070 (t0)
REVERT: D  340 LYS cc_start: 0.8470 (mtpm) cc_final: 0.8133 (mttt)
REVERT: D  373 THR cc_start: 0.8600 (m) cc_final: 0.8378 (p)
REVERT: E  311 LYS cc_start: 0.8192 (mtmt) cc_final: 0.7814 (mmtt)
REVERT: E  331 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8734 (mtmm)
REVERT: E  340 LYS cc_start: 0.8353 (mtpm) cc_final: 0.8011 (mttt)
REVERT: E  349 ARG cc_start: 0.8737 (mtt180) cc_final: 0.7311 (mmp-170)
REVERT: E  375 LYS cc_start: 0.8121 (tttt) cc_final: 0.7873 (tptm)
REVERT: F  311 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7651 (mmtt)
REVERT: F  340 LYS cc_start: 0.8353 (mtpm) cc_final: 0.7961 (mttt)
REVERT: F  347 LYS cc_start: 0.8815 (mptt) cc_final: 0.8586 (mptp)
  outliers start: 6
  outliers final: 1
  residues processed: 123
  average time/residue: 1.4371
  time to fit residues: 180.7269
Evaluate side-chains
  118 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 115
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 LYS
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain E residue  331 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 8 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0870
   chunk 27 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   chunk 38 optimal weight:    6.9990
   chunk 15 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 19 optimal weight:    8.9990
   overall best weight:    2.1764

-------------------------------------------------------------------------------
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 = 0.4195 r_free = 0.4195 target = 0.155702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.113691 restraints weight = 3636.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.3706 rms_B_bonded: 1.80
r_work: 0.3593 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3505 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8791
moved from start:          0.3221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3498  Z= 0.218
  Angle     :  0.562   9.699   4680  Z= 0.278
  Chirality :  0.049   0.155    528
  Planarity :  0.002   0.014    594
  Dihedral  :  4.653  15.319    462
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 24.49 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.34), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.23 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS E 329 
 PHE   0.008   0.001   PHE A 346 
 TYR   0.010   0.003   TYR B 310 
 ARG   0.001   0.000   ARG B 379 

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 116
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8434 (mtmt)
REVERT: A  340 LYS cc_start: 0.8331 (mtpm) cc_final: 0.8047 (mttt)
REVERT: A  375 LYS cc_start: 0.7927 (tttt) cc_final: 0.7669 (tptm)
REVERT: B  311 LYS cc_start: 0.8422 (mtmt) cc_final: 0.7395 (pptt)
REVERT: B  338 GLU cc_start: 0.8533 (tt0) cc_final: 0.8113 (tt0)
REVERT: B  340 LYS cc_start: 0.8650 (mtpm) cc_final: 0.8228 (mtmt)
REVERT: B  375 LYS cc_start: 0.8298 (tttm) cc_final: 0.7837 (tppp)
REVERT: C  340 LYS cc_start: 0.8375 (mtpm) cc_final: 0.7957 (mttt)
REVERT: C  373 THR cc_start: 0.8467 (m) cc_final: 0.8036 (p)
REVERT: C  375 LYS cc_start: 0.8162 (tttt) cc_final: 0.7853 (tttm)
REVERT: D  311 LYS cc_start: 0.8463 (mtmt) cc_final: 0.7391 (pptt)
REVERT: D  340 LYS cc_start: 0.8488 (mtpm) cc_final: 0.8145 (mttt)
REVERT: D  373 THR cc_start: 0.8599 (m) cc_final: 0.8353 (p)
REVERT: E  311 LYS cc_start: 0.8207 (mtmt) cc_final: 0.7803 (mmtt)
REVERT: E  331 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8718 (mtmm)
REVERT: E  340 LYS cc_start: 0.8362 (mtpm) cc_final: 0.8009 (mttt)
REVERT: E  349 ARG cc_start: 0.8727 (mtt180) cc_final: 0.7311 (mmp-170)
REVERT: E  375 LYS cc_start: 0.8155 (tttt) cc_final: 0.7767 (tttm)
REVERT: F  311 LYS cc_start: 0.8103 (mtmt) cc_final: 0.7660 (mmtt)
REVERT: F  340 LYS cc_start: 0.8365 (mtpm) cc_final: 0.7982 (mttt)
REVERT: F  347 LYS cc_start: 0.8837 (mptt) cc_final: 0.8607 (mptp)
  outliers start: 4
  outliers final: 1
  residues processed: 120
  average time/residue: 1.3911
  time to fit residues: 170.8138
Evaluate side-chains
  118 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 115
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 LYS
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain E residue  331 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 29 optimal weight:    9.9990
   chunk 16 optimal weight:    7.9990
   chunk 22 optimal weight:    0.0870
   chunk 40 optimal weight:    7.9990
   chunk 23 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 10 optimal weight:    8.9990
   overall best weight:    1.6164

-------------------------------------------------------------------------------
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 = 0.4206 r_free = 0.4206 target = 0.156719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.114840 restraints weight = 3621.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3724 rms_B_bonded: 1.79
r_work: 0.3612 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3525 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8779
moved from start:          0.3299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3498  Z= 0.172
  Angle     :  0.535   9.626   4680  Z= 0.264
  Chirality :  0.049   0.128    528
  Planarity :  0.002   0.014    594
  Dihedral  :  4.525  14.655    462
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 24.24 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.34), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.20 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS E 329 
 PHE   0.007   0.001   PHE A 346 
 TYR   0.010   0.002   TYR B 310 
 ARG   0.001   0.000   ARG D 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4402.21 seconds
wall clock time: 78 minutes 15.71 seconds (4695.71 seconds total)