Starting phenix.real_space_refine
on Wed Sep 17 03:50:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ern_19927/09_2025/9ern_19927.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ern_19927/09_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_19927/09_2025/9ern_19927.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ern_19927/09_2025/9ern_19927.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ern_19927/09_2025/9ern_19927.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ern_19927/09_2025/9ern_19927.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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:
    B, C, D, E, F
  Time building chain proxies: 0.56, per 1000 atoms: 0.16
  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: 0.20
  Conformation dependent library (CDL) restraints added in 135.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.14
  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: 0.43

  Time building geometry restraints manager: 0.27 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  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:             4.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.220
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.150
-------------------------------------------------------------------------------
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= 0.575
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.001   0.000   ARG E 379 
 TYR   0.036   0.011   TYR B 310 
 PHE   0.026   0.006   PHE E 346 
 HIS   0.012   0.004   HIS B 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00888 ( 3498)
  covalent geometry    : angle       1.37914 ( 4680)
  hydrogen bonds       : bond        0.17191 (   60)
  hydrogen bonds       : angle       8.47861 (  180)

*********************** 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  : 0.143 
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: 0.6728
  time to fit residues: 97.5454
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  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    7.9990
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    7.9990
   chunk 25 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    9.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
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 330 HIS
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: 19

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.157016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.115150 restraints weight = 3633.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.3696 rms_B_bonded: 1.82
r_work: 0.3577 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3487 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8780
moved from start:          0.2177

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= 0.186
  Angle     :  0.626   4.027   4680  Z= 0.332
  Chirality :  0.051   0.133    528
  Planarity :  0.004   0.032    594
  Dihedral  :  5.167  15.928    462
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 2.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 14.90 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.16 (0.32), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.64 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 349 
 TYR   0.018   0.004   TYR B 310 
 PHE   0.011   0.002   PHE A 346 
 HIS   0.003   0.001   HIS B 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 3498)
  covalent geometry    : angle       0.62606 ( 4680)
  hydrogen bonds       : bond        0.03116 (   60)
  hydrogen bonds       : angle       6.56705 (  180)

*********************** 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
  145 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 138
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.8424 (mtpm) cc_final: 0.8001 (mttp)
REVERT: A  375 LYS cc_start: 0.8098 (tttt) cc_final: 0.7734 (tttm)
REVERT: B  311 LYS cc_start: 0.8524 (mtmt) cc_final: 0.7033 (pptt)
REVERT: B  338 GLU cc_start: 0.8548 (tt0) cc_final: 0.8265 (tt0)
REVERT: B  340 LYS cc_start: 0.8678 (mtpm) cc_final: 0.8284 (mttt)
REVERT: B  347 LYS cc_start: 0.8943 (mptt) cc_final: 0.8722 (mptp)
REVERT: C  340 LYS cc_start: 0.8448 (mtpm) cc_final: 0.8026 (mttt)
REVERT: C  345 ASP cc_start: 0.8413 (m-30) cc_final: 0.8010 (t0)
REVERT: C  373 THR cc_start: 0.8392 (m) cc_final: 0.7969 (p)
REVERT: C  375 LYS cc_start: 0.8265 (tttt) cc_final: 0.7911 (tttm)
REVERT: D  311 LYS cc_start: 0.8464 (mtmt) cc_final: 0.7121 (pptt)
REVERT: D  317 LYS cc_start: 0.8564 (pttt) cc_final: 0.8291 (ptpt)
REVERT: D  321 LYS cc_start: 0.8608 (ttpt) cc_final: 0.8353 (mtmm)
REVERT: D  340 LYS cc_start: 0.8617 (mtpm) cc_final: 0.8260 (mttt)
REVERT: D  373 THR cc_start: 0.8645 (m) cc_final: 0.8369 (p)
REVERT: D  375 LYS cc_start: 0.8679 (tttt) cc_final: 0.7673 (pmtt)
REVERT: E  311 LYS cc_start: 0.8092 (mtmt) cc_final: 0.7658 (mmtt)
REVERT: E  340 LYS cc_start: 0.8435 (mtpm) cc_final: 0.8054 (mttt)
REVERT: E  349 ARG cc_start: 0.8734 (mtt180) cc_final: 0.7295 (mtp180)
REVERT: E  375 LYS cc_start: 0.8145 (tttt) cc_final: 0.7707 (tttm)
REVERT: F  311 LYS cc_start: 0.8008 (mtmt) cc_final: 0.7520 (mmtt)
REVERT: F  340 LYS cc_start: 0.8465 (mtpm) cc_final: 0.8021 (mttt)
REVERT: F  347 LYS cc_start: 0.8810 (mptt) cc_final: 0.8530 (mptp)
REVERT: F  373 THR cc_start: 0.8452 (m) cc_final: 0.7959 (p)
REVERT: F  375 LYS cc_start: 0.8106 (tttt) cc_final: 0.7785 (tttt)
  outliers start: 7
  outliers final: 1
  residues processed: 142
  average time/residue: 0.6706
  time to fit residues: 97.2709
Evaluate side-chains
  126 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
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 0 optimal weight:   10.0000
   chunk 26 optimal weight:    9.9990
   chunk 8 optimal weight:    9.9990
   chunk 9 optimal weight:    8.9990
   chunk 31 optimal weight:    2.9990
   chunk 34 optimal weight:    9.9990
   chunk 2 optimal weight:   10.0000
   chunk 32 optimal weight:    7.9990
   chunk 20 optimal weight:    9.9990
   chunk 14 optimal weight:   10.0000
   chunk 11 optimal weight:    1.9990
   overall best weight:    6.3990

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.152298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.110467 restraints weight = 3632.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 1.81
r_work: 0.3508 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3416 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8832
moved from start:          0.2603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.060   3498  Z= 0.357
  Angle     :  0.764   6.008   4680  Z= 0.403
  Chirality :  0.056   0.145    528
  Planarity :  0.004   0.020    594
  Dihedral  :  5.470  17.685    462
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 19.44 %
    Favored  : 76.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.00 (0.33), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.52 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 349 
 TYR   0.019   0.005   TYR A 310 
 PHE   0.012   0.002   PHE A 346 
 HIS   0.004   0.001   HIS C 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00837 ( 3498)
  covalent geometry    : angle       0.76358 ( 4680)
  hydrogen bonds       : bond        0.04132 (   60)
  hydrogen bonds       : angle       6.48081 (  180)

*********************** 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
  146 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.8495 (mtpm) cc_final: 0.8033 (mttp)
REVERT: A  375 LYS cc_start: 0.8061 (tttt) cc_final: 0.7678 (tttm)
REVERT: B  311 LYS cc_start: 0.8507 (mtmt) cc_final: 0.7278 (pptt)
REVERT: B  331 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8739 (mtmt)
REVERT: B  340 LYS cc_start: 0.8677 (mtpm) cc_final: 0.8206 (mttt)
REVERT: B  347 LYS cc_start: 0.8974 (mptt) cc_final: 0.8709 (mptp)
REVERT: B  373 THR cc_start: 0.8806 (m) cc_final: 0.8478 (p)
REVERT: C  340 LYS cc_start: 0.8467 (mtpm) cc_final: 0.7998 (mtmt)
REVERT: C  373 THR cc_start: 0.8507 (m) cc_final: 0.8127 (p)
REVERT: C  375 LYS cc_start: 0.8341 (tttt) cc_final: 0.8016 (tttm)
REVERT: D  311 LYS cc_start: 0.8494 (mtmt) cc_final: 0.7233 (pptt)
REVERT: D  340 LYS cc_start: 0.8573 (mtpm) cc_final: 0.8214 (mttt)
REVERT: D  373 THR cc_start: 0.8726 (m) cc_final: 0.8425 (p)
REVERT: E  311 LYS cc_start: 0.8323 (mtmt) cc_final: 0.7873 (mmtt)
REVERT: E  340 LYS cc_start: 0.8434 (mtpm) cc_final: 0.8037 (mttt)
REVERT: E  349 ARG cc_start: 0.8734 (mtt180) cc_final: 0.7227 (mtp180)
REVERT: E  375 LYS cc_start: 0.8201 (tttt) cc_final: 0.7769 (tttm)
REVERT: F  311 LYS cc_start: 0.8143 (mtmt) cc_final: 0.7646 (mmtt)
REVERT: F  340 LYS cc_start: 0.8420 (mtpm) cc_final: 0.7998 (mttt)
REVERT: F  347 LYS cc_start: 0.8822 (mptt) cc_final: 0.8583 (mptp)
REVERT: F  349 ARG cc_start: 0.8723 (mtt180) cc_final: 0.6970 (tpt90)
REVERT: F  373 THR cc_start: 0.8483 (m) cc_final: 0.8066 (p)
  outliers start: 15
  outliers final: 5
  residues processed: 137
  average time/residue: 0.6737
  time to fit residues: 94.2731
Evaluate side-chains
  136 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 130
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  331 LYS
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain E residue  317 LYS
Chi-restraints excluded: chain E residue  319 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 14 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 35 optimal weight:    7.9990
   chunk 9 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    2.3990

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.155494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.113611 restraints weight = 3597.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.3678 rms_B_bonded: 1.80
r_work: 0.3565 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3476 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8802
moved from start:          0.2858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3498  Z= 0.151
  Angle     :  0.570   4.759   4680  Z= 0.294
  Chirality :  0.050   0.131    528
  Planarity :  0.003   0.016    594
  Dihedral  :  5.010  15.824    462
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 22.22 %
    Favored  : 75.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.001   0.000   ARG F 349 
 TYR   0.013   0.003   TYR B 310 
 PHE   0.007   0.001   PHE A 346 
 HIS   0.002   0.001   HIS E 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 3498)
  covalent geometry    : angle       0.57046 ( 4680)
  hydrogen bonds       : bond        0.02578 (   60)
  hydrogen bonds       : angle       6.01069 (  180)

*********************** 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
  140 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8437 (mtmt)
REVERT: A  340 LYS cc_start: 0.8372 (mtpm) cc_final: 0.7973 (mttp)
REVERT: A  375 LYS cc_start: 0.7960 (tttt) cc_final: 0.7533 (tttm)
REVERT: B  311 LYS cc_start: 0.8428 (mtmt) cc_final: 0.7329 (pptt)
REVERT: B  338 GLU cc_start: 0.8514 (tt0) cc_final: 0.8046 (tt0)
REVERT: B  340 LYS cc_start: 0.8679 (mtpm) cc_final: 0.8237 (mtmt)
REVERT: B  347 LYS cc_start: 0.8914 (mptt) cc_final: 0.8689 (mptp)
REVERT: B  375 LYS cc_start: 0.8313 (tttm) cc_final: 0.7853 (tppp)
REVERT: C  340 LYS cc_start: 0.8421 (mtpm) cc_final: 0.7985 (mttt)
REVERT: C  373 THR cc_start: 0.8468 (m) cc_final: 0.8062 (p)
REVERT: C  375 LYS cc_start: 0.8285 (tttt) cc_final: 0.7953 (tttm)
REVERT: D  311 LYS cc_start: 0.8408 (mtmt) cc_final: 0.7268 (pptt)
REVERT: D  340 LYS cc_start: 0.8493 (mtpm) cc_final: 0.8157 (mttt)
REVERT: D  373 THR cc_start: 0.8656 (m) cc_final: 0.8393 (p)
REVERT: E  311 LYS cc_start: 0.8187 (mtmt) cc_final: 0.7826 (mmtt)
REVERT: E  331 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8725 (mtmm)
REVERT: E  340 LYS cc_start: 0.8413 (mtpm) cc_final: 0.8059 (mttt)
REVERT: E  349 ARG cc_start: 0.8734 (mtt180) cc_final: 0.7328 (mmp-170)
REVERT: E  375 LYS cc_start: 0.8174 (tttt) cc_final: 0.7784 (tttm)
REVERT: F  311 LYS cc_start: 0.8049 (mtmt) cc_final: 0.7591 (mmtt)
REVERT: F  340 LYS cc_start: 0.8397 (mtpm) cc_final: 0.8015 (mttt)
REVERT: F  347 LYS cc_start: 0.8823 (mptt) cc_final: 0.8597 (mptp)
REVERT: F  349 ARG cc_start: 0.8745 (mtt180) cc_final: 0.7023 (tpt90)
REVERT: F  373 THR cc_start: 0.8505 (m) cc_final: 0.8153 (p)
REVERT: F  375 LYS cc_start: 0.8084 (tttt) cc_final: 0.7859 (tttm)
  outliers start: 10
  outliers final: 2
  residues processed: 134
  average time/residue: 0.6876
  time to fit residues: 94.0246
Evaluate side-chains
  133 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 129
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
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  331 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 21 optimal weight:    9.9990
   chunk 17 optimal weight:    9.9990
   chunk 32 optimal weight:    6.9990
   chunk 24 optimal weight:    8.9990
   chunk 28 optimal weight:    6.9990
   chunk 6 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 0 optimal weight:    8.9990
   chunk 41 optimal weight:    1.9990
   chunk 26 optimal weight:    7.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    5.9990

-------------------------------------------------------------------------------
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 = 0.4132 r_free = 0.4132 target = 0.151334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.109299 restraints weight = 3669.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 1.84
r_work: 0.3503 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3412 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8843
moved from start:          0.2835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.059   3498  Z= 0.337
  Angle     :  0.730   5.862   4680  Z= 0.379
  Chirality :  0.054   0.141    528
  Planarity :  0.003   0.015    594
  Dihedral  :  5.394  17.360    462
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 2.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 21.46 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.85 (0.33), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.40 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 349 
 TYR   0.017   0.005   TYR C 310 
 PHE   0.011   0.002   PHE A 346 
 HIS   0.003   0.001   HIS B 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00790 ( 3498)
  covalent geometry    : angle       0.72955 ( 4680)
  hydrogen bonds       : bond        0.03673 (   60)
  hydrogen bonds       : angle       6.24966 (  180)

*********************** 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
  142 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8574 (mtmt)
REVERT: A  340 LYS cc_start: 0.8471 (mtpm) cc_final: 0.8033 (mttp)
REVERT: A  373 THR cc_start: 0.8488 (m) cc_final: 0.7951 (p)
REVERT: A  375 LYS cc_start: 0.8019 (tttt) cc_final: 0.7647 (tttm)
REVERT: B  311 LYS cc_start: 0.8499 (mtmt) cc_final: 0.7401 (pptt)
REVERT: B  340 LYS cc_start: 0.8655 (mtpm) cc_final: 0.8220 (mttt)
REVERT: B  347 LYS cc_start: 0.9001 (mptt) cc_final: 0.8775 (mptp)
REVERT: B  373 THR cc_start: 0.8829 (m) cc_final: 0.8563 (p)
REVERT: C  340 LYS cc_start: 0.8483 (mtpm) cc_final: 0.8027 (mtmt)
REVERT: C  373 THR cc_start: 0.8510 (m) cc_final: 0.8067 (p)
REVERT: C  375 LYS cc_start: 0.8362 (tttt) cc_final: 0.8041 (tttm)
REVERT: D  311 LYS cc_start: 0.8536 (mtmt) cc_final: 0.7331 (pptt)
REVERT: D  340 LYS cc_start: 0.8565 (mtpm) cc_final: 0.8188 (mttt)
REVERT: D  373 THR cc_start: 0.8690 (m) cc_final: 0.8401 (p)
REVERT: E  311 LYS cc_start: 0.8332 (mtmt) cc_final: 0.7966 (mmtt)
REVERT: E  331 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8735 (mtmm)
REVERT: E  340 LYS cc_start: 0.8445 (mtpm) cc_final: 0.8072 (mttt)
REVERT: E  349 ARG cc_start: 0.8758 (mtt180) cc_final: 0.7346 (mtp180)
REVERT: E  375 LYS cc_start: 0.8200 (tttt) cc_final: 0.7784 (tttm)
REVERT: F  311 LYS cc_start: 0.8157 (mtmt) cc_final: 0.7669 (mmtt)
REVERT: F  340 LYS cc_start: 0.8422 (mtpm) cc_final: 0.8018 (mttt)
REVERT: F  347 LYS cc_start: 0.8877 (mptt) cc_final: 0.8670 (mptp)
REVERT: F  349 ARG cc_start: 0.8765 (mtt180) cc_final: 0.7300 (mmp-170)
  outliers start: 14
  outliers final: 4
  residues processed: 132
  average time/residue: 0.6898
  time to fit residues: 92.8985
Evaluate side-chains
  130 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 124
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
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  306 VAL
Chi-restraints excluded: chain E residue  331 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 33 optimal weight:    0.1980
   chunk 14 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 13 optimal weight:    7.9990
   chunk 9 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 7 optimal weight:   10.0000
   chunk 31 optimal weight:    8.9990
   chunk 15 optimal weight:    8.9990
   overall best weight:    1.6186

-------------------------------------------------------------------------------
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 = 0.4190 r_free = 0.4190 target = 0.156318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.114555 restraints weight = 3578.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.3698 rms_B_bonded: 1.80
r_work: 0.3584 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3495 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8789
moved from start:          0.3055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3498  Z= 0.112
  Angle     :  0.524   4.476   4680  Z= 0.268
  Chirality :  0.049   0.130    528
  Planarity :  0.002   0.012    594
  Dihedral  :  4.846  14.806    462
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 1.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 23.48 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.72 (0.34), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.30 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 379 
 TYR   0.012   0.003   TYR B 310 
 PHE   0.005   0.001   PHE A 346 
 HIS   0.002   0.001   HIS E 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 3498)
  covalent geometry    : angle       0.52352 ( 4680)
  hydrogen bonds       : bond        0.02175 (   60)
  hydrogen bonds       : angle       5.82341 (  180)

*********************** 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
  127 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 123
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.8377 (mtpm) cc_final: 0.8059 (mttt)
REVERT: A  375 LYS cc_start: 0.7929 (tttt) cc_final: 0.7724 (tptm)
REVERT: B  311 LYS cc_start: 0.8437 (mtmt) cc_final: 0.7370 (pptt)
REVERT: B  340 LYS cc_start: 0.8661 (mtpm) cc_final: 0.8222 (mtmt)
REVERT: B  347 LYS cc_start: 0.8880 (mptt) cc_final: 0.8677 (mptp)
REVERT: B  375 LYS cc_start: 0.8302 (tttm) cc_final: 0.7841 (tppp)
REVERT: C  340 LYS cc_start: 0.8375 (mtpm) cc_final: 0.7969 (mtmt)
REVERT: C  373 THR cc_start: 0.8469 (m) cc_final: 0.8057 (p)
REVERT: C  375 LYS cc_start: 0.8270 (tttt) cc_final: 0.7951 (tttm)
REVERT: D  311 LYS cc_start: 0.8419 (mtmt) cc_final: 0.7310 (pptt)
REVERT: D  314 ASP cc_start: 0.8419 (t0) cc_final: 0.8154 (t0)
REVERT: D  340 LYS cc_start: 0.8468 (mtpm) cc_final: 0.8123 (mttt)
REVERT: D  373 THR cc_start: 0.8614 (m) cc_final: 0.8394 (p)
REVERT: D  375 LYS cc_start: 0.8649 (tttt) cc_final: 0.8344 (tttm)
REVERT: E  311 LYS cc_start: 0.8174 (mtmt) cc_final: 0.7794 (mmtt)
REVERT: E  331 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8723 (mtmm)
REVERT: E  340 LYS cc_start: 0.8398 (mtpm) cc_final: 0.8046 (mttt)
REVERT: E  349 ARG cc_start: 0.8715 (mtt180) cc_final: 0.7285 (mmp-170)
REVERT: E  375 LYS cc_start: 0.8136 (tttt) cc_final: 0.7889 (tptm)
REVERT: F  311 LYS cc_start: 0.8101 (mtmt) cc_final: 0.7643 (mmtt)
REVERT: F  340 LYS cc_start: 0.8374 (mtpm) cc_final: 0.7988 (mttt)
REVERT: F  347 LYS cc_start: 0.8841 (mptt) cc_final: 0.8635 (mptp)
REVERT: F  373 THR cc_start: 0.8520 (m) cc_final: 0.8131 (p)
  outliers start: 4
  outliers final: 1
  residues processed: 125
  average time/residue: 0.6950
  time to fit residues: 88.7359
Evaluate side-chains
  123 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 121
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  320 SER
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 21 optimal weight:    9.9990
   chunk 28 optimal weight:    3.9990
   chunk 9 optimal weight:    7.9990
   chunk 7 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9980
   chunk 40 optimal weight:    0.1980
   chunk 26 optimal weight:    9.9990
   chunk 8 optimal weight:   10.0000
   chunk 3 optimal weight:    9.9990
   chunk 15 optimal weight:    9.9990
   overall best weight:    4.6386

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.152503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.110358 restraints weight = 3689.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3645 rms_B_bonded: 1.84
r_work: 0.3527 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3438 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8829
moved from start:          0.2987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   3498  Z= 0.262
  Angle     :  0.659   5.068   4680  Z= 0.337
  Chirality :  0.052   0.136    528
  Planarity :  0.003   0.014    594
  Dihedral  :  5.210  16.327    462
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 22.98 %
    Favored  : 74.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.74 (0.34), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.32 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 379 
 TYR   0.015   0.004   TYR A 310 
 PHE   0.009   0.002   PHE A 346 
 HIS   0.002   0.001   HIS B 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00613 ( 3498)
  covalent geometry    : angle       0.65877 ( 4680)
  hydrogen bonds       : bond        0.03122 (   60)
  hydrogen bonds       : angle       6.09432 (  180)

*********************** 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
  134 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 123
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8570 (mtmt)
REVERT: A  340 LYS cc_start: 0.8436 (mtpm) cc_final: 0.7987 (mttp)
REVERT: A  375 LYS cc_start: 0.7994 (tttt) cc_final: 0.7748 (tptm)
REVERT: B  311 LYS cc_start: 0.8489 (mtmt) cc_final: 0.7380 (pptt)
REVERT: B  340 LYS cc_start: 0.8658 (mtpm) cc_final: 0.8227 (mttt)
REVERT: B  347 LYS cc_start: 0.9002 (mptt) cc_final: 0.8789 (mptp)
REVERT: B  373 THR cc_start: 0.8792 (m) cc_final: 0.8526 (p)
REVERT: C  340 LYS cc_start: 0.8457 (mtpm) cc_final: 0.8008 (mtmt)
REVERT: C  373 THR cc_start: 0.8505 (m) cc_final: 0.8110 (p)
REVERT: C  375 LYS cc_start: 0.8318 (tttt) cc_final: 0.8003 (tttm)
REVERT: D  311 LYS cc_start: 0.8498 (mtmt) cc_final: 0.7380 (pptt)
REVERT: D  340 LYS cc_start: 0.8526 (mtpm) cc_final: 0.8153 (mttt)
REVERT: D  373 THR cc_start: 0.8673 (m) cc_final: 0.8393 (p)
REVERT: D  375 LYS cc_start: 0.8671 (tttt) cc_final: 0.8364 (tttm)
REVERT: E  311 LYS cc_start: 0.8276 (mtmt) cc_final: 0.7874 (mmtt)
REVERT: E  331 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8730 (mtmm)
REVERT: E  340 LYS cc_start: 0.8423 (mtpm) cc_final: 0.8047 (mttt)
REVERT: E  349 ARG cc_start: 0.8759 (mtt180) cc_final: 0.7322 (mtp180)
REVERT: E  375 LYS cc_start: 0.8161 (tttt) cc_final: 0.7755 (tttm)
REVERT: F  311 LYS cc_start: 0.8122 (mtmt) cc_final: 0.7671 (mmtt)
REVERT: F  340 LYS cc_start: 0.8406 (mtpm) cc_final: 0.8003 (mttt)
REVERT: F  347 LYS cc_start: 0.8878 (mptt) cc_final: 0.8674 (mptp)
REVERT: F  349 ARG cc_start: 0.8763 (mtt180) cc_final: 0.7028 (tpt90)
  outliers start: 11
  outliers final: 2
  residues processed: 128
  average time/residue: 0.6815
  time to fit residues: 89.0499
Evaluate side-chains
  128 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 124
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
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  331 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 13 optimal weight:    9.9990
   chunk 39 optimal weight:    4.9990
   chunk 34 optimal weight:   20.0000
   chunk 19 optimal weight:    0.9980
   chunk 7 optimal weight:   10.0000
   chunk 37 optimal weight:    6.9990
   chunk 15 optimal weight:    9.9990
   chunk 11 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 4 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   overall best weight:    2.5386

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.155069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.113109 restraints weight = 3661.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 1.83
r_work: 0.3559 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3470 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8804
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3498  Z= 0.154
  Angle     :  0.578   8.796   4680  Z= 0.289
  Chirality :  0.050   0.169    528
  Planarity :  0.002   0.013    594
  Dihedral  :  4.925  15.350    462
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 1.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 23.48 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.69 (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
 ARG   0.001   0.000   ARG D 379 
 TYR   0.012   0.003   TYR B 310 
 PHE   0.007   0.001   PHE A 346 
 HIS   0.001   0.000   HIS E 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 3498)
  covalent geometry    : angle       0.57756 ( 4680)
  hydrogen bonds       : bond        0.02406 (   60)
  hydrogen bonds       : angle       5.87584 (  180)

*********************** 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
  129 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 122
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8543 (mtmt)
REVERT: A  340 LYS cc_start: 0.8401 (mtpm) cc_final: 0.8055 (mttt)
REVERT: A  375 LYS cc_start: 0.7942 (tttt) cc_final: 0.7719 (tptm)
REVERT: B  311 LYS cc_start: 0.8449 (mtmt) cc_final: 0.7397 (pptt)
REVERT: B  340 LYS cc_start: 0.8674 (mtpm) cc_final: 0.8226 (mttt)
REVERT: B  347 LYS cc_start: 0.8916 (mptt) cc_final: 0.8684 (mptp)
REVERT: B  375 LYS cc_start: 0.8316 (tttm) cc_final: 0.7846 (tppp)
REVERT: C  340 LYS cc_start: 0.8397 (mtpm) cc_final: 0.7972 (mtmt)
REVERT: C  373 THR cc_start: 0.8477 (m) cc_final: 0.8064 (p)
REVERT: C  375 LYS cc_start: 0.8218 (tttt) cc_final: 0.7900 (tttm)
REVERT: D  311 LYS cc_start: 0.8490 (mtmt) cc_final: 0.7402 (pptt)
REVERT: D  314 ASP cc_start: 0.8416 (t0) cc_final: 0.8111 (t0)
REVERT: D  340 LYS cc_start: 0.8490 (mtpm) cc_final: 0.8144 (mttt)
REVERT: D  373 THR cc_start: 0.8612 (m) cc_final: 0.8364 (p)
REVERT: D  375 LYS cc_start: 0.8656 (tttt) cc_final: 0.8344 (tttm)
REVERT: E  311 LYS cc_start: 0.8183 (mtmt) cc_final: 0.7825 (mmtt)
REVERT: E  331 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8728 (mtmm)
REVERT: E  340 LYS cc_start: 0.8392 (mtpm) cc_final: 0.8037 (mttt)
REVERT: E  349 ARG cc_start: 0.8727 (mtt180) cc_final: 0.7285 (mmp-170)
REVERT: E  375 LYS cc_start: 0.8129 (tttt) cc_final: 0.7734 (tttm)
REVERT: F  311 LYS cc_start: 0.8138 (mtmt) cc_final: 0.7654 (mmtt)
REVERT: F  340 LYS cc_start: 0.8372 (mtpm) cc_final: 0.7979 (mttt)
REVERT: F  347 LYS cc_start: 0.8857 (mptt) cc_final: 0.8647 (mptp)
REVERT: F  349 ARG cc_start: 0.8762 (mtt180) cc_final: 0.7030 (tpt90)
  outliers start: 7
  outliers final: 3
  residues processed: 126
  average time/residue: 0.7142
  time to fit residues: 91.7898
Evaluate side-chains
  125 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 120
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ILE
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  331 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 33 optimal weight:    9.9990
   chunk 37 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 20 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 17 optimal weight:    6.9990
   chunk 18 optimal weight:    3.9990
   chunk 31 optimal weight:    8.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    2.7588

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.154699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.112685 restraints weight = 3629.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3680 rms_B_bonded: 1.81
r_work: 0.3566 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3476 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8805
moved from start:          0.3123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3498  Z= 0.166
  Angle     :  0.596  10.421   4680  Z= 0.296
  Chirality :  0.051   0.188    528
  Planarity :  0.002   0.014    594
  Dihedral  :  4.930  15.174    462
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 2.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 22.98 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.67 (0.34), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.26 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 379 
 TYR   0.012   0.003   TYR B 310 
 PHE   0.007   0.001   PHE A 346 
 HIS   0.001   0.000   HIS E 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 3498)
  covalent geometry    : angle       0.59600 ( 4680)
  hydrogen bonds       : bond        0.02477 (   60)
  hydrogen bonds       : angle       5.87610 (  180)

*********************** 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
  131 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 123
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8540 (mtmt)
REVERT: A  340 LYS cc_start: 0.8393 (mtpm) cc_final: 0.8054 (mttt)
REVERT: A  375 LYS cc_start: 0.7938 (tttt) cc_final: 0.7711 (tptm)
REVERT: B  311 LYS cc_start: 0.8468 (mtmt) cc_final: 0.7404 (pptt)
REVERT: B  340 LYS cc_start: 0.8667 (mtpm) cc_final: 0.8228 (mttt)
REVERT: B  347 LYS cc_start: 0.8917 (mptt) cc_final: 0.8686 (mptp)
REVERT: B  375 LYS cc_start: 0.8325 (tttm) cc_final: 0.7882 (tppp)
REVERT: C  340 LYS cc_start: 0.8403 (mtpm) cc_final: 0.7978 (mtmt)
REVERT: C  373 THR cc_start: 0.8477 (m) cc_final: 0.8063 (p)
REVERT: C  375 LYS cc_start: 0.8203 (tttt) cc_final: 0.7870 (tttm)
REVERT: D  311 LYS cc_start: 0.8484 (mtmt) cc_final: 0.7406 (pptt)
REVERT: D  314 ASP cc_start: 0.8450 (t0) cc_final: 0.8138 (t0)
REVERT: D  340 LYS cc_start: 0.8493 (mtpm) cc_final: 0.8144 (mttt)
REVERT: D  373 THR cc_start: 0.8611 (m) cc_final: 0.8355 (p)
REVERT: D  375 LYS cc_start: 0.8621 (tttt) cc_final: 0.8310 (tttm)
REVERT: E  311 LYS cc_start: 0.8227 (mtmt) cc_final: 0.7853 (mmtt)
REVERT: E  331 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8732 (mtmm)
REVERT: E  340 LYS cc_start: 0.8403 (mtpm) cc_final: 0.8041 (mttt)
REVERT: E  349 ARG cc_start: 0.8727 (mtt180) cc_final: 0.7306 (mmp-170)
REVERT: E  375 LYS cc_start: 0.8135 (tttt) cc_final: 0.7743 (tttm)
REVERT: F  311 LYS cc_start: 0.8136 (mtmt) cc_final: 0.7671 (mmtt)
REVERT: F  340 LYS cc_start: 0.8378 (mtpm) cc_final: 0.7974 (mttt)
REVERT: F  347 LYS cc_start: 0.8859 (mptt) cc_final: 0.8648 (mptp)
REVERT: F  349 ARG cc_start: 0.8758 (mtt180) cc_final: 0.7032 (tpt90)
REVERT: F  375 LYS cc_start: 0.8039 (tttm) cc_final: 0.7661 (tppp)
  outliers start: 8
  outliers final: 4
  residues processed: 127
  average time/residue: 0.6975
  time to fit residues: 90.4449
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  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ILE
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  306 VAL
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 34 optimal weight:    3.9990
   chunk 37 optimal weight:    7.9990
   chunk 21 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 30 optimal weight:    9.9990
   chunk 16 optimal weight:    7.9990
   chunk 7 optimal weight:   10.0000
   chunk 28 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    3.1186

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.154523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.112410 restraints weight = 3656.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3667 rms_B_bonded: 1.83
r_work: 0.3550 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3462 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8811
moved from start:          0.3168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3498  Z= 0.184
  Angle     :  0.614  10.392   4680  Z= 0.305
  Chirality :  0.051   0.193    528
  Planarity :  0.002   0.014    594
  Dihedral  :  4.981  16.013    462
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 22.73 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.66 (0.34), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.25 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 379 
 TYR   0.013   0.003   TYR B 310 
 PHE   0.007   0.002   PHE A 346 
 HIS   0.001   0.000   HIS E 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 3498)
  covalent geometry    : angle       0.61375 ( 4680)
  hydrogen bonds       : bond        0.02586 (   60)
  hydrogen bonds       : angle       5.90840 (  180)

********************** 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
  129 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 122
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8526 (mtmt)
REVERT: A  340 LYS cc_start: 0.8411 (mtpm) cc_final: 0.8061 (mttt)
REVERT: A  375 LYS cc_start: 0.7947 (tttt) cc_final: 0.7722 (tptm)
REVERT: B  311 LYS cc_start: 0.8475 (mtmt) cc_final: 0.7411 (pptt)
REVERT: B  340 LYS cc_start: 0.8663 (mtpm) cc_final: 0.8226 (mttt)
REVERT: B  347 LYS cc_start: 0.8921 (mptt) cc_final: 0.8718 (mptp)
REVERT: B  375 LYS cc_start: 0.8330 (tttm) cc_final: 0.7887 (tppp)
REVERT: C  340 LYS cc_start: 0.8412 (mtpm) cc_final: 0.7987 (mtmt)
REVERT: C  373 THR cc_start: 0.8491 (m) cc_final: 0.8084 (p)
REVERT: C  375 LYS cc_start: 0.8185 (tttt) cc_final: 0.7859 (tttm)
REVERT: D  311 LYS cc_start: 0.8487 (mtmt) cc_final: 0.7475 (pptt)
REVERT: D  314 ASP cc_start: 0.8473 (t0) cc_final: 0.8160 (t0)
REVERT: D  340 LYS cc_start: 0.8513 (mtpm) cc_final: 0.8150 (mttt)
REVERT: D  373 THR cc_start: 0.8636 (m) cc_final: 0.8377 (p)
REVERT: D  375 LYS cc_start: 0.8624 (tttt) cc_final: 0.8315 (tttm)
REVERT: E  311 LYS cc_start: 0.8255 (mtmt) cc_final: 0.7856 (mmtt)
REVERT: E  331 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8740 (mtmm)
REVERT: E  340 LYS cc_start: 0.8409 (mtpm) cc_final: 0.8048 (mttt)
REVERT: E  349 ARG cc_start: 0.8739 (mtt180) cc_final: 0.7307 (mmp-170)
REVERT: E  375 LYS cc_start: 0.8125 (tttt) cc_final: 0.7724 (tttm)
REVERT: F  311 LYS cc_start: 0.8142 (mtmt) cc_final: 0.7677 (mmtt)
REVERT: F  340 LYS cc_start: 0.8376 (mtpm) cc_final: 0.7973 (mttt)
REVERT: F  347 LYS cc_start: 0.8856 (mptt) cc_final: 0.8651 (mptp)
REVERT: F  349 ARG cc_start: 0.8769 (mtt180) cc_final: 0.7036 (tpt90)
REVERT: F  375 LYS cc_start: 0.8084 (tttm) cc_final: 0.7706 (tppp)
  outliers start: 7
  outliers final: 4
  residues processed: 125
  average time/residue: 0.7229
  time to fit residues: 92.1940
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  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ILE
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  306 VAL
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 1 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9980
   chunk 3 optimal weight:    7.9990
   chunk 8 optimal weight:   10.0000
   chunk 24 optimal weight:    2.9990
   chunk 33 optimal weight:    8.9990
   chunk 30 optimal weight:    0.9990
   chunk 35 optimal weight:    6.9990
   chunk 29 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0050
   overall best weight:    1.6000

-------------------------------------------------------------------------------
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 = 0.4197 r_free = 0.4197 target = 0.156591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.114796 restraints weight = 3659.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 1.79
r_work: 0.3598 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3511 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8784
moved from start:          0.3300

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= 0.107
  Angle     :  0.534   9.671   4680  Z= 0.264
  Chirality :  0.049   0.143    528
  Planarity :  0.002   0.015    594
  Dihedral  :  4.657  14.481    462
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 1.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 23.74 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.58 (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
 ARG   0.001   0.000   ARG D 379 
 TYR   0.011   0.002   TYR B 310 
 PHE   0.005   0.001   PHE A 346 
 HIS   0.002   0.000   HIS E 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 3498)
  covalent geometry    : angle       0.53407 ( 4680)
  hydrogen bonds       : bond        0.01991 (   60)
  hydrogen bonds       : angle       5.68805 (  180)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2302.07 seconds
wall clock time: 40 minutes 2.25 seconds (2402.25 seconds total)