Starting phenix.real_space_refine
on Tue Mar  3 16:07:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qkj_14044/03_2026/7qkj_14044.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qkj_14044/03_2026/7qkj_14044.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qkj_14044/03_2026/7qkj_14044.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qkj_14044/03_2026/7qkj_14044.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qkj_14044/03_2026/7qkj_14044.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qkj_14044/03_2026/7qkj_14044.map"
  }
  resolution = 3.26
  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=   0.002
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      12      5.16       5
     C    4320      2.51       5
     N    1272      2.21       5
     O    1284      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6888
  Number of models: 1
  Model: ""
    Number of chains: 12
    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}
    Chain: "B"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "C"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "D"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "E"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "F"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "G"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "H"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "I"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "J"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "K"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "L"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
  Time building chain proxies: 1.48, per 1000 atoms: 0.21
  Number of scatterers: 6888
  At special positions: 0
  Unit cell: (159.032, 189.52, 46.144, 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      12     16.00
     O    1284      8.00
     N    1272      7.00
     C    4320      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: 0.66
  Conformation dependent library (CDL) restraints added in 252.4 milliseconds
  

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1584

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 37 sheets defined
      0.0% alpha, 37.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310
      removed outlier: 6.409A  pdb=" N   GLN A 307 " --> pdb=" O   ILE C 308 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   TYR C 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   VAL A 309 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   VAL B 306 " --> pdb=" O   GLN C 307 " (cutoff:3.500A)
      removed outlier: 7.839A  pdb=" N   VAL C 309 " --> pdb=" O   VAL B 306 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   ILE B 308 " --> pdb=" O   VAL C 309 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314
      removed outlier: 6.765A  pdb=" N   VAL A 313 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 319 through 322
      removed outlier: 6.768A  pdb=" N   THR A 319 " --> pdb=" O   SER C 320 " (cutoff:3.500A)
      removed outlier: 8.278A  pdb=" N   CYS C 322 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   LYS A 321 " --> pdb=" O   CYS C 322 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 329
      removed outlier: 6.372A  pdb=" N   ILE A 328 " --> pdb=" O   HIS C 329 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 337 through 341
      removed outlier: 6.574A  pdb=" N   GLU A 338 " --> pdb=" O   VAL C 339 " (cutoff:3.500A)
      removed outlier: 7.943A  pdb=" N   SER C 341 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   LYS A 340 " --> pdb=" O   SER C 341 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   VAL B 337 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   LYS C 340 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   VAL B 339 " --> pdb=" O   LYS C 340 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 346
      removed outlier: 6.650A  pdb=" N   ASP A 345 " --> pdb=" O   PHE C 346 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 350 through 354
      removed outlier: 6.422A  pdb=" N   VAL B 350 " --> pdb=" O   GLN C 351 " (cutoff:3.500A)
      removed outlier: 8.498A  pdb=" N   LYS C 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 361
      removed outlier: 6.391A  pdb=" N   ASP A 358 " --> pdb=" O   ASN C 359 " (cutoff:3.500A)
      removed outlier: 8.048A  pdb=" N   THR C 361 " --> pdb=" O   ASP A 358 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   ILE A 360 " --> pdb=" O   THR C 361 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 368 through 371
    Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 377
      removed outlier: 6.509A  pdb=" N   HIS B 374 " --> pdb=" O   LYS C 375 " (cutoff:3.500A)
      removed outlier: 8.181A  pdb=" N   THR C 377 " --> pdb=" O   HIS B 374 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   LEU B 376 " --> pdb=" O   THR C 377 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 307 through 310
      removed outlier: 6.352A  pdb=" N   ILE D 308 " --> pdb=" O   VAL E 309 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 313 through 314
      removed outlier: 6.799A  pdb=" N   VAL D 313 " --> pdb=" O   ASP F 314 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 319 through 322
      removed outlier: 6.724A  pdb=" N   THR D 319 " --> pdb=" O   SER F 320 " (cutoff:3.500A)
      removed outlier: 8.429A  pdb=" N   CYS F 322 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   LYS D 321 " --> pdb=" O   CYS F 322 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 328 through 329
      removed outlier: 6.423A  pdb=" N   ILE D 328 " --> pdb=" O   HIS F 329 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 337 through 341
      removed outlier: 6.521A  pdb=" N   VAL D 337 " --> pdb=" O   GLU E 338 " (cutoff:3.500A)
      removed outlier: 8.021A  pdb=" N   LYS E 340 " --> pdb=" O   VAL D 337 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   VAL D 339 " --> pdb=" O   LYS E 340 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 345 through 346
      removed outlier: 6.770A  pdb=" N   ASP D 345 " --> pdb=" O   PHE F 346 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 350 through 358
      removed outlier: 6.924A  pdb=" N   LEU E 357 " --> pdb=" O   SER D 356 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   ASP D 358 " --> pdb=" O   LEU E 357 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   SER F 356 " --> pdb=" O   GLY D 355 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   LEU D 357 " --> pdb=" O   SER F 356 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   ASP F 358 " --> pdb=" O   LEU D 357 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 368 through 371
      removed outlier: 6.483A  pdb=" N   ASN D 368 " --> pdb=" O   LYS E 369 " (cutoff:3.500A)
      removed outlier: 7.945A  pdb=" N   ILE E 371 " --> pdb=" O   ASN D 368 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   LYS D 370 " --> pdb=" O   ILE E 371 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 374 through 377
      removed outlier: 6.687A  pdb=" N   HIS D 374 " --> pdb=" O   LYS E 375 " (cutoff:3.500A)
      removed outlier: 8.246A  pdb=" N   THR E 377 " --> pdb=" O   HIS D 374 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   LEU D 376 " --> pdb=" O   THR E 377 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'H' and resid 306 through 310
      removed outlier: 6.432A  pdb=" N   VAL G 306 " --> pdb=" O   GLN H 307 " (cutoff:3.500A)
      removed outlier: 7.806A  pdb=" N   VAL H 309 " --> pdb=" O   VAL G 306 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   ILE G 308 " --> pdb=" O   VAL H 309 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   GLN G 307 " --> pdb=" O   ILE I 308 " (cutoff:3.500A)
      removed outlier: 7.711A  pdb=" N   TYR I 310 " --> pdb=" O   GLN G 307 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   VAL G 309 " --> pdb=" O   TYR I 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC2
    Processing sheet with id=AC3, first strand: chain 'H' and resid 313 through 314
      removed outlier: 6.881A  pdb=" N   VAL G 313 " --> pdb=" O   ASP I 314 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'H' and resid 319 through 322
      removed outlier: 6.819A  pdb=" N   THR G 319 " --> pdb=" O   SER I 320 " (cutoff:3.500A)
      removed outlier: 8.437A  pdb=" N   CYS I 322 " --> pdb=" O   THR G 319 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   LYS G 321 " --> pdb=" O   CYS I 322 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'H' and resid 328 through 329
      removed outlier: 6.438A  pdb=" N   ILE G 328 " --> pdb=" O   HIS I 329 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'H' and resid 337 through 341
      removed outlier: 6.646A  pdb=" N   VAL G 337 " --> pdb=" O   GLU H 338 " (cutoff:3.500A)
      removed outlier: 8.235A  pdb=" N   LYS H 340 " --> pdb=" O   VAL G 337 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   VAL G 339 " --> pdb=" O   LYS H 340 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'H' and resid 345 through 346
      removed outlier: 6.629A  pdb=" N   ASP G 345 " --> pdb=" O   PHE I 346 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'H' and resid 350 through 358
      removed outlier: 6.278A  pdb=" N   VAL G 350 " --> pdb=" O   GLN H 351 " (cutoff:3.500A)
      removed outlier: 8.162A  pdb=" N   LYS H 353 " --> pdb=" O   VAL G 350 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   SER G 352 " --> pdb=" O   LYS H 353 " (cutoff:3.500A)
      removed outlier: 8.689A  pdb=" N   GLY H 355 " --> pdb=" O   SER G 352 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   ILE G 354 " --> pdb=" O   GLY H 355 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   LEU H 357 " --> pdb=" O   ILE G 354 " (cutoff:3.500A)
      removed outlier: 7.363A  pdb=" N   SER G 356 " --> pdb=" O   LEU H 357 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   SER I 356 " --> pdb=" O   GLY G 355 " (cutoff:3.500A)
      removed outlier: 7.047A  pdb=" N   LEU G 357 " --> pdb=" O   SER I 356 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   ASP I 358 " --> pdb=" O   LEU G 357 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'H' and resid 368 through 377
      removed outlier: 6.608A  pdb=" N   LYS G 369 " --> pdb=" O   LYS I 370 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   GLU I 372 " --> pdb=" O   LYS G 369 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   ILE G 371 " --> pdb=" O   GLU I 372 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   HIS I 374 " --> pdb=" O   ILE G 371 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   THR G 373 " --> pdb=" O   HIS I 374 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   LEU I 376 " --> pdb=" O   THR G 373 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   LYS G 375 " --> pdb=" O   LEU I 376 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'K' and resid 306 through 310
    Processing sheet with id=AD2, first strand: chain 'K' and resid 313 through 314
      removed outlier: 6.783A  pdb=" N   VAL J 313 " --> pdb=" O   ASP L 314 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'K' and resid 319 through 322
      removed outlier: 6.683A  pdb=" N   THR J 319 " --> pdb=" O   SER L 320 " (cutoff:3.500A)
      removed outlier: 8.358A  pdb=" N   CYS L 322 " --> pdb=" O   THR J 319 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   LYS J 321 " --> pdb=" O   CYS L 322 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'K' and resid 328 through 329
      removed outlier: 6.504A  pdb=" N   ILE J 328 " --> pdb=" O   HIS L 329 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'K' and resid 337 through 341
    Processing sheet with id=AD6, first strand: chain 'K' and resid 345 through 346
      removed outlier: 6.664A  pdb=" N   ASP J 345 " --> pdb=" O   PHE L 346 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'K' and resid 350 through 354
      removed outlier: 6.416A  pdb=" N   VAL J 350 " --> pdb=" O   GLN K 351 " (cutoff:3.500A)
      removed outlier: 8.487A  pdb=" N   LYS K 353 " --> pdb=" O   VAL J 350 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   SER J 352 " --> pdb=" O   LYS K 353 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'K' and resid 357 through 361
      removed outlier: 6.312A  pdb=" N   ASP J 358 " --> pdb=" O   ASN L 359 " (cutoff:3.500A)
      removed outlier: 7.933A  pdb=" N   THR L 361 " --> pdb=" O   ASP J 358 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   ILE J 360 " --> pdb=" O   THR L 361 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'K' and resid 368 through 371
      removed outlier: 6.550A  pdb=" N   LYS J 369 " --> pdb=" O   LYS L 370 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'K' and resid 374 through 377
      removed outlier: 6.476A  pdb=" N   HIS J 374 " --> pdb=" O   LYS K 375 " (cutoff:3.500A)
      removed outlier: 8.156A  pdb=" N   THR K 377 " --> pdb=" O   HIS J 374 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   LEU J 376 " --> pdb=" O   THR K 377 " (cutoff:3.500A)

    113 hydrogen bonds defined for protein.
    339 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: 0.89

  Time building geometry restraints manager: 0.81 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 1982
        1.34 -     1.46: 867
        1.46 -     1.58: 4132
        1.58 -     1.70: 3
        1.70 -     1.82: 12
  Bond restraints: 6996
  Sorted by residual:
  bond pdb=" CA  GLU J 372 "
       pdb=" CB  GLU J 372 "
    ideal  model  delta    sigma   weight residual
    1.527  1.566 -0.039 7.60e-03 1.73e+04 2.63e+01
  bond pdb=" N   GLY L 355 "
       pdb=" CA  GLY L 355 "
    ideal  model  delta    sigma   weight residual
    1.442  1.468 -0.026 7.70e-03 1.69e+04 1.15e+01
  bond pdb=" CA  ILE K 371 "
       pdb=" CB  ILE K 371 "
    ideal  model  delta    sigma   weight residual
    1.538  1.582 -0.044 1.30e-02 5.92e+03 1.12e+01
  bond pdb=" CZ  ARG K 379 "
       pdb=" NH2 ARG K 379 "
    ideal  model  delta    sigma   weight residual
    1.330  1.293  0.037 1.30e-02 5.92e+03 8.12e+00
  bond pdb=" CZ  ARG J 379 "
       pdb=" NH2 ARG J 379 "
    ideal  model  delta    sigma   weight residual
    1.330  1.293  0.037 1.30e-02 5.92e+03 8.03e+00
  ... (remaining 6991 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.92: 8895
        3.92 -     7.84: 440
        7.84 -    11.76: 11
       11.76 -    15.68: 10
       15.68 -    19.61: 4
  Bond angle restraints: 9360
  Sorted by residual:
  angle pdb=" N   GLU B 372 "
        pdb=" CA  GLU B 372 "
        pdb=" C   GLU B 372 "
      ideal   model   delta    sigma   weight residual
     110.44  125.38  -14.94 1.20e+00 6.94e-01 1.55e+02
  angle pdb=" N   GLU C 372 "
        pdb=" CA  GLU C 372 "
        pdb=" C   GLU C 372 "
      ideal   model   delta    sigma   weight residual
     110.44  124.79  -14.35 1.20e+00 6.94e-01 1.43e+02
  angle pdb=" N   ASN F 327 "
        pdb=" CA  ASN F 327 "
        pdb=" C   ASN F 327 "
      ideal   model   delta    sigma   weight residual
     110.35  126.12  -15.77 1.36e+00 5.41e-01 1.35e+02
  angle pdb=" CA  ILE J 371 "
        pdb=" CB  ILE J 371 "
        pdb=" CG1 ILE J 371 "
      ideal   model   delta    sigma   weight residual
     110.40  130.01  -19.61 1.70e+00 3.46e-01 1.33e+02
  angle pdb=" N   GLU A 372 "
        pdb=" CA  GLU A 372 "
        pdb=" C   GLU A 372 "
      ideal   model   delta    sigma   weight residual
     110.88  124.29  -13.41 1.28e+00 6.10e-01 1.10e+02
  ... (remaining 9355 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.61: 3493
       10.61 -    21.23: 552
       21.23 -    31.84: 169
       31.84 -    42.46: 43
       42.46 -    53.07: 15
  Dihedral angle restraints: 4272
    sinusoidal: 1788
      harmonic: 2484
  Sorted by residual:
  dihedral pdb=" C   GLU L 372 "
           pdb=" N   GLU L 372 "
           pdb=" CA  GLU L 372 "
           pdb=" CB  GLU L 372 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -151.85   29.25     0      2.50e+00 1.60e-01 1.37e+02
  dihedral pdb=" C   GLU B 372 "
           pdb=" N   GLU B 372 "
           pdb=" CA  GLU B 372 "
           pdb=" CB  GLU B 372 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -151.00   28.40     0      2.50e+00 1.60e-01 1.29e+02
  dihedral pdb=" C   GLU C 372 "
           pdb=" N   GLU C 372 "
           pdb=" CA  GLU C 372 "
           pdb=" CB  GLU C 372 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -150.98   28.38     0      2.50e+00 1.60e-01 1.29e+02
  ... (remaining 4269 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.259: 1029
       0.259 -    0.519: 14
       0.519 -    0.778: 2
       0.778 -    1.037: 2
       1.037 -    1.297: 9
  Chirality restraints: 1056
  Sorted by residual:
  chirality pdb=" CA  GLU L 372 "
            pdb=" N   GLU L 372 "
            pdb=" C   GLU L 372 "
            pdb=" CB  GLU L 372 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.21    1.30 2.00e-01 2.50e+01 4.20e+01
  chirality pdb=" CA  ASN F 327 "
            pdb=" N   ASN F 327 "
            pdb=" C   ASN F 327 "
            pdb=" CB  ASN F 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.26    1.25 2.00e-01 2.50e+01 3.92e+01
  chirality pdb=" CA  GLU B 372 "
            pdb=" N   GLU B 372 "
            pdb=" C   GLU B 372 "
            pdb=" CB  GLU B 372 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.28    1.23 2.00e-01 2.50e+01 3.79e+01
  ... (remaining 1053 not shown)

  Planarity restraints: 1188
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN D 359 "    0.024 2.00e-02 2.50e+03   4.56e-02 2.08e+01
        pdb=" C   ASN D 359 "   -0.079 2.00e-02 2.50e+03
        pdb=" O   ASN D 359 "    0.029 2.00e-02 2.50e+03
        pdb=" N   ILE D 360 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN F 359 "    0.022 2.00e-02 2.50e+03   4.33e-02 1.87e+01
        pdb=" C   ASN F 359 "   -0.075 2.00e-02 2.50e+03
        pdb=" O   ASN F 359 "    0.028 2.00e-02 2.50e+03
        pdb=" N   ILE F 360 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN E 359 "    0.022 2.00e-02 2.50e+03   4.30e-02 1.85e+01
        pdb=" C   ASN E 359 "   -0.074 2.00e-02 2.50e+03
        pdb=" O   ASN E 359 "    0.027 2.00e-02 2.50e+03
        pdb=" N   ILE E 360 "    0.025 2.00e-02 2.50e+03
  ... (remaining 1185 not shown)

  Histogram of nonbonded interaction distances:
        2.51 -     2.99: 3200
        2.99 -     3.47: 5386
        3.47 -     3.94: 11041
        3.94 -     4.42: 10462
        4.42 -     4.90: 20856
  Nonbonded interactions: 50945
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP E 314 "
            pdb=" OG  SER E 316 "
     model   vdw
     2.510 3.040
  nonbonded pdb=" OD1 ASP D 314 "
            pdb=" OG  SER D 316 "
     model   vdw
     2.527 3.040
  nonbonded pdb=" OD1 ASP K 314 "
            pdb=" OG  SER K 316 "
     model   vdw
     2.538 3.040
  nonbonded pdb=" OD1 ASP A 314 "
            pdb=" OG  SER A 316 "
     model   vdw
     2.552 3.040
  nonbonded pdb=" OD1 ASP J 314 "
            pdb=" OG  SER J 316 "
     model   vdw
     2.570 3.040
  ... (remaining 50940 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
}

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:             3.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.340
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6904
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      :  0.012   0.058   6996  Z= 0.770
  Angle     :  2.043  19.606   9360  Z= 1.314
  Chirality :  0.155   1.297   1056
  Planarity :  0.010   0.068   1188
  Dihedral  : 11.594  53.069   2688
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 0.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.93 %
    Favored  : 90.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Cbeta Deviations :  1.52 %
  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 are not related in a simple way.
  whole: -2.24 (0.25), residues: 876
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.70 (0.19), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L 349 
 TYR   0.042   0.010   TYR B 310 
 PHE   0.034   0.009   PHE E 346 
 HIS   0.011   0.003   HIS G 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.01205 ( 6996)
  covalent geometry    : angle       2.04255 ( 9360)
  hydrogen bonds       : bond        0.12305 (  113)
  hydrogen bonds       : angle       8.02264 (  339)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 232
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  349 ARG cc_start: 0.7128 (ttm170) cc_final: 0.6421 (mmp-170)
REVERT: K  349 ARG cc_start: 0.8266 (ttm170) cc_final: 0.6674 (mmp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 232
  average time/residue: 0.1278
  time to fit residues: 35.6633
Evaluate side-chains
  159 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.0170
   chunk 45 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.1222

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

Flipped N/Q/H residues before XYZ refinement:
A 329 HIS
C 330 HIS
C 368 ASN
D 327 ASN
E 327 ASN
F 327 ASN
H 307 GLN
H 336 GLN
I 336 GLN
L 327 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4894 r_free = 0.4894 target = 0.243896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.171931 restraints weight = 7360.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.4355 rms_B_bonded: 1.88
r_work: 0.4263 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.4167 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.4167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.3371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6996  Z= 0.121
  Angle     :  0.634   7.378   9360  Z= 0.325
  Chirality :  0.048   0.178   1056
  Planarity :  0.004   0.034   1188
  Dihedral  :  5.564  16.676    924
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.79 %
    Favored  : 91.21 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 11.49 %
    Favored  : 86.74 %
  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 are not related in a simple way.
  whole: -2.12 (0.26), residues: 876
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.60 (0.19), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L 349 
 TYR   0.007   0.001   TYR G 310 
 PHE   0.007   0.001   PHE H 346 
 HIS   0.004   0.001   HIS D 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 6996)
  covalent geometry    : angle       0.63408 ( 9360)
  hydrogen bonds       : bond        0.02344 (  113)
  hydrogen bonds       : angle       6.24314 (  339)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 184
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  375 LYS cc_start: 0.7430 (tttt) cc_final: 0.6971 (mmmt)
REVERT: D  311 LYS cc_start: 0.8602 (ttmt) cc_final: 0.8234 (mmtt)
REVERT: D  325 LEU cc_start: 0.8370 (tt) cc_final: 0.8170 (mp)
REVERT: E  349 ARG cc_start: 0.8549 (ttm170) cc_final: 0.6766 (mmp-170)
REVERT: G  340 LYS cc_start: 0.7726 (ptmt) cc_final: 0.7160 (mttt)
REVERT: G  348 ASP cc_start: 0.7309 (t0) cc_final: 0.7072 (t70)
REVERT: G  371 ILE cc_start: 0.8508 (mm) cc_final: 0.8299 (mm)
REVERT: H  349 ARG cc_start: 0.6718 (ttm170) cc_final: 0.5434 (mmp-170)
REVERT: H  369 LYS cc_start: 0.5558 (tptt) cc_final: 0.4590 (ttmm)
REVERT: I  331 LYS cc_start: 0.7663 (ttmt) cc_final: 0.6641 (pttt)
REVERT: I  340 LYS cc_start: 0.7067 (ptmt) cc_final: 0.6801 (pttp)
REVERT: I  349 ARG cc_start: 0.6981 (ttm170) cc_final: 0.5534 (ptt-90)
REVERT: J  325 LEU cc_start: 0.8014 (tt) cc_final: 0.7773 (mt)
REVERT: J  349 ARG cc_start: 0.8040 (ttm-80) cc_final: 0.7791 (ttm110)
REVERT: J  357 LEU cc_start: 0.9017 (tt) cc_final: 0.8813 (tp)
REVERT: K  340 LYS cc_start: 0.7900 (mttm) cc_final: 0.7579 (mptt)
REVERT: K  349 ARG cc_start: 0.7986 (ttm170) cc_final: 0.6540 (mmp-170)
REVERT: K  372 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7098 (tm-30)
  outliers start: 14
  outliers final: 5
  residues processed: 193
  average time/residue: 0.1074
  time to fit residues: 25.6006
Evaluate side-chains
  166 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 161
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  373 THR
Chi-restraints excluded: chain H residue  354 ILE
Chi-restraints excluded: chain L residue  324 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 2 optimal weight:   20.0000
   chunk 7 optimal weight:   40.0000
   chunk 57 optimal weight:    8.9990
   chunk 62 optimal weight:   10.0000
   chunk 42 optimal weight:   30.0000
   chunk 19 optimal weight:   30.0000
   chunk 82 optimal weight:    9.9990
   chunk 9 optimal weight:    0.5980
   chunk 76 optimal weight:    1.9990
   chunk 6 optimal weight:   30.0000
   chunk 81 optimal weight:    0.9980
   overall best weight:    4.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 330 HIS
D 327 ASN
E 359 ASN
F 327 ASN
G 307 GLN
H 307 GLN
K 327 ASN
L 307 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4776 r_free = 0.4776 target = 0.238558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.165924 restraints weight = 7431.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.4205 rms_B_bonded: 1.76
r_work: 0.4113 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.4019 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.4019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.4130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   6996  Z= 0.216
  Angle     :  0.706   7.031   9360  Z= 0.366
  Chirality :  0.052   0.182   1056
  Planarity :  0.004   0.044   1188
  Dihedral  :  5.553  18.782    924
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 13.51 %
    Favored  : 84.09 %
  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 are not related in a simple way.
  whole: -2.19 (0.25), residues: 876
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.66 (0.19), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 349 
 TYR   0.011   0.002   TYR G 310 
 PHE   0.009   0.001   PHE K 346 
 HIS   0.006   0.001   HIS F 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00515 ( 6996)
  covalent geometry    : angle       0.70594 ( 9360)
  hydrogen bonds       : bond        0.02713 (  113)
  hydrogen bonds       : angle       6.07849 (  339)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 174
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  321 LYS cc_start: 0.4955 (mttt) cc_final: 0.3980 (tmtt)
REVERT: E  311 LYS cc_start: 0.6765 (mmtm) cc_final: 0.5583 (mmtm)
REVERT: F  325 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8291 (mp)
REVERT: F  372 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7903 (tt0)
REVERT: G  325 LEU cc_start: 0.6426 (mt) cc_final: 0.6173 (mt)
REVERT: G  340 LYS cc_start: 0.7924 (ptmt) cc_final: 0.7465 (mttt)
REVERT: H  317 LYS cc_start: 0.6853 (tttt) cc_final: 0.6227 (tppt)
REVERT: H  328 ILE cc_start: 0.6638 (mm) cc_final: 0.6407 (mt)
REVERT: H  349 ARG cc_start: 0.6992 (ttm170) cc_final: 0.5641 (mmp-170)
REVERT: H  369 LYS cc_start: 0.5829 (tptt) cc_final: 0.4614 (ttmm)
REVERT: K  340 LYS cc_start: 0.7973 (mttm) cc_final: 0.7676 (mptt)
REVERT: K  349 ARG cc_start: 0.8067 (ttm170) cc_final: 0.6687 (mmp-170)
REVERT: L  349 ARG cc_start: 0.8324 (ttm-80) cc_final: 0.8011 (mtp85)
  outliers start: 19
  outliers final: 11
  residues processed: 181
  average time/residue: 0.1045
  time to fit residues: 23.7903
Evaluate side-chains
  174 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 161
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  325 LEU
Chi-restraints excluded: chain F residue  372 GLU
Chi-restraints excluded: chain F residue  373 THR
Chi-restraints excluded: chain G residue  339 VAL
Chi-restraints excluded: chain G residue  371 ILE
Chi-restraints excluded: chain I residue  337 VAL
Chi-restraints excluded: chain I residue  356 SER
Chi-restraints excluded: chain L residue  324 SER
Chi-restraints excluded: chain L residue  356 SER
Chi-restraints excluded: chain L residue  357 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 50 optimal weight:   20.0000
   chunk 82 optimal weight:    9.9990
   chunk 51 optimal weight:   20.0000
   chunk 28 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 78 optimal weight:   10.0000
   chunk 47 optimal weight:    0.0970
   chunk 18 optimal weight:   20.0000
   chunk 53 optimal weight:    8.9990
   chunk 38 optimal weight:    0.7980
   chunk 46 optimal weight:    5.9990
   overall best weight:    2.5784

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

Flipped N/Q/H residues before XYZ refinement:
H 307 GLN
J 327 ASN
L 307 GLN
L 327 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4826 r_free = 0.4826 target = 0.228975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.156256 restraints weight = 7306.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.4277 rms_B_bonded: 1.80
r_work: 0.4186 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.4093 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.4093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.4706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6996  Z= 0.136
  Angle     :  0.589   5.557   9360  Z= 0.303
  Chirality :  0.048   0.237   1056
  Planarity :  0.004   0.038   1188
  Dihedral  :  4.922  14.950    924
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 14.90 %
    Favored  : 82.32 %
  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 are not related in a simple way.
  whole: -2.24 (0.25), residues: 876
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.70 (0.19), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 349 
 TYR   0.010   0.001   TYR G 310 
 PHE   0.005   0.001   PHE D 378 
 HIS   0.004   0.001   HIS D 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 6996)
  covalent geometry    : angle       0.58862 ( 9360)
  hydrogen bonds       : bond        0.02152 (  113)
  hydrogen bonds       : angle       5.79776 (  339)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 173
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  321 LYS cc_start: 0.4651 (mttt) cc_final: 0.4215 (tmtt)
REVERT: B  328 ILE cc_start: 0.5049 (OUTLIER) cc_final: 0.4583 (mm)
REVERT: C  321 LYS cc_start: 0.6373 (ptpt) cc_final: 0.5904 (ptmt)
REVERT: D  372 GLU cc_start: 0.8187 (tt0) cc_final: 0.7903 (tt0)
REVERT: E  311 LYS cc_start: 0.6262 (mmtm) cc_final: 0.5529 (ptmt)
REVERT: F  372 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7870 (tt0)
REVERT: G  338 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7502 (mm-30)
REVERT: G  340 LYS cc_start: 0.7823 (ptmt) cc_final: 0.7411 (mttt)
REVERT: G  349 ARG cc_start: 0.7179 (mtp85) cc_final: 0.6276 (mmm-85)
REVERT: H  317 LYS cc_start: 0.6873 (tttt) cc_final: 0.6294 (tppt)
REVERT: H  328 ILE cc_start: 0.6594 (mm) cc_final: 0.6380 (mt)
REVERT: H  347 LYS cc_start: 0.7582 (tttt) cc_final: 0.7048 (mmtp)
REVERT: H  349 ARG cc_start: 0.7027 (ttm170) cc_final: 0.5501 (mmp-170)
REVERT: I  336 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6865 (tt0)
REVERT: I  349 ARG cc_start: 0.6912 (ttm170) cc_final: 0.5347 (ptt-90)
REVERT: K  311 LYS cc_start: 0.8670 (ttpt) cc_final: 0.7929 (mmtm)
REVERT: K  340 LYS cc_start: 0.7949 (mttm) cc_final: 0.7650 (mptt)
REVERT: K  349 ARG cc_start: 0.7961 (ttm170) cc_final: 0.6756 (mmp-170)
REVERT: K  372 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7102 (tm-30)
REVERT: L  340 LYS cc_start: 0.8607 (tttt) cc_final: 0.8371 (mttp)
  outliers start: 22
  outliers final: 12
  residues processed: 185
  average time/residue: 0.1127
  time to fit residues: 25.8782
Evaluate side-chains
  177 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 161
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  372 GLU
Chi-restraints excluded: chain F residue  373 THR
Chi-restraints excluded: chain H residue  371 ILE
Chi-restraints excluded: chain I residue  325 LEU
Chi-restraints excluded: chain I residue  336 GLN
Chi-restraints excluded: chain I residue  337 VAL
Chi-restraints excluded: chain I residue  356 SER
Chi-restraints excluded: chain J residue  324 SER
Chi-restraints excluded: chain J residue  325 LEU
Chi-restraints excluded: chain K residue  372 GLU
Chi-restraints excluded: chain L residue  316 SER
Chi-restraints excluded: chain L residue  324 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 14 optimal weight:    0.0040
   chunk 63 optimal weight:   10.0000
   chunk 73 optimal weight:    9.9990
   chunk 5 optimal weight:   30.0000
   chunk 21 optimal weight:   10.0000
   chunk 15 optimal weight:   20.0000
   chunk 67 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 39 optimal weight:    7.9990
   chunk 48 optimal weight:   30.0000
   chunk 44 optimal weight:    6.9990
   overall best weight:    3.9998

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

Flipped N/Q/H residues before XYZ refinement:
H 307 GLN
L 307 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4784 r_free = 0.4784 target = 0.227739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.155978 restraints weight = 7166.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.4222 rms_B_bonded: 1.82
r_work: 0.4123 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.4028 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.4028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.5101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6996  Z= 0.190
  Angle     :  0.638   6.319   9360  Z= 0.328
  Chirality :  0.050   0.194   1056
  Planarity :  0.004   0.040   1188
  Dihedral  :  5.084  15.717    924
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 15.15 %
    Favored  : 81.44 %
  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 are not related in a simple way.
  whole: -2.25 (0.25), residues: 876
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.71 (0.19), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 349 
 TYR   0.012   0.002   TYR D 310 
 PHE   0.007   0.001   PHE K 346 
 HIS   0.004   0.001   HIS F 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 6996)
  covalent geometry    : angle       0.63759 ( 9360)
  hydrogen bonds       : bond        0.02357 (  113)
  hydrogen bonds       : angle       5.88320 (  339)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 150
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  328 ILE cc_start: 0.5024 (OUTLIER) cc_final: 0.4517 (mm)
REVERT: C  321 LYS cc_start: 0.6413 (ptpt) cc_final: 0.6029 (ptmt)
REVERT: F  372 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8033 (tt0)
REVERT: G  338 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7543 (mm-30)
REVERT: G  340 LYS cc_start: 0.7892 (ptmt) cc_final: 0.7506 (mttt)
REVERT: G  349 ARG cc_start: 0.7274 (mtp85) cc_final: 0.7030 (mtp85)
REVERT: H  317 LYS cc_start: 0.6964 (tttt) cc_final: 0.6280 (tppt)
REVERT: H  328 ILE cc_start: 0.6513 (mm) cc_final: 0.6265 (mt)
REVERT: H  347 LYS cc_start: 0.7546 (tttt) cc_final: 0.6885 (mmtp)
REVERT: H  349 ARG cc_start: 0.6977 (ttm170) cc_final: 0.5594 (mmp-170)
REVERT: H  370 LYS cc_start: 0.5994 (ttpt) cc_final: 0.5535 (tmtt)
REVERT: I  336 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.6914 (tt0)
REVERT: I  349 ARG cc_start: 0.6645 (ttm170) cc_final: 0.5309 (ptt-90)
REVERT: K  340 LYS cc_start: 0.7964 (mttm) cc_final: 0.7646 (mptt)
REVERT: K  372 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7135 (tm-30)
REVERT: L  340 LYS cc_start: 0.8666 (tttt) cc_final: 0.8374 (mttp)
  outliers start: 27
  outliers final: 17
  residues processed: 163
  average time/residue: 0.1022
  time to fit residues: 20.9893
Evaluate side-chains
  168 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 147
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain E residue  327 ASN
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  372 GLU
Chi-restraints excluded: chain F residue  373 THR
Chi-restraints excluded: chain G residue  356 SER
Chi-restraints excluded: chain G residue  371 ILE
Chi-restraints excluded: chain I residue  336 GLN
Chi-restraints excluded: chain I residue  337 VAL
Chi-restraints excluded: chain I residue  354 ILE
Chi-restraints excluded: chain I residue  356 SER
Chi-restraints excluded: chain J residue  324 SER
Chi-restraints excluded: chain J residue  325 LEU
Chi-restraints excluded: chain K residue  325 LEU
Chi-restraints excluded: chain K residue  372 GLU
Chi-restraints excluded: chain L residue  316 SER
Chi-restraints excluded: chain L residue  324 SER
Chi-restraints excluded: chain L residue  356 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 82 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 23 optimal weight:   10.0000
   chunk 44 optimal weight:   20.0000
   chunk 76 optimal weight:    4.9990
   chunk 24 optimal weight:   10.0000
   chunk 4 optimal weight:   20.0000
   chunk 74 optimal weight:    0.9980
   chunk 19 optimal weight:   30.0000
   chunk 59 optimal weight:    3.9990
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 327 ASN
C 330 HIS
I 359 ASN
L 307 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4820 r_free = 0.4820 target = 0.241902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.167349 restraints weight = 7438.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.4265 rms_B_bonded: 1.86
r_work: 0.4169 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.4071 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.4071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.5407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6996  Z= 0.136
  Angle     :  0.587   6.922   9360  Z= 0.300
  Chirality :  0.048   0.163   1056
  Planarity :  0.004   0.036   1188
  Dihedral  :  4.737  15.612    924
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 17.05 %
    Favored  : 80.18 %
  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 are not related in a simple way.
  whole: -2.31 (0.25), residues: 876
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.75 (0.19), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG J 349 
 TYR   0.009   0.001   TYR D 310 
 PHE   0.005   0.001   PHE D 378 
 HIS   0.003   0.001   HIS D 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 6996)
  covalent geometry    : angle       0.58700 ( 9360)
  hydrogen bonds       : bond        0.02017 (  113)
  hydrogen bonds       : angle       5.66391 (  339)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 158
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  328 ILE cc_start: 0.5005 (OUTLIER) cc_final: 0.4491 (mm)
REVERT: C  321 LYS cc_start: 0.6566 (ptpt) cc_final: 0.6180 (ptmt)
REVERT: D  372 GLU cc_start: 0.8191 (tt0) cc_final: 0.7865 (tt0)
REVERT: F  372 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7895 (tt0)
REVERT: G  338 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7567 (mm-30)
REVERT: G  340 LYS cc_start: 0.7808 (ptmt) cc_final: 0.7441 (mttt)
REVERT: G  349 ARG cc_start: 0.7362 (mtp85) cc_final: 0.7158 (mtp85)
REVERT: H  317 LYS cc_start: 0.7021 (tttt) cc_final: 0.6318 (tppt)
REVERT: H  328 ILE cc_start: 0.6590 (mm) cc_final: 0.6304 (mt)
REVERT: H  347 LYS cc_start: 0.7526 (tttt) cc_final: 0.6900 (mmtp)
REVERT: H  349 ARG cc_start: 0.6973 (ttm170) cc_final: 0.5521 (mmp-170)
REVERT: H  370 LYS cc_start: 0.5972 (ttpt) cc_final: 0.5706 (tmtt)
REVERT: I  336 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.6815 (tt0)
REVERT: I  349 ARG cc_start: 0.6520 (ttm170) cc_final: 0.5243 (ptt-90)
REVERT: J  340 LYS cc_start: 0.8256 (mptt) cc_final: 0.8031 (mptt)
REVERT: K  311 LYS cc_start: 0.8678 (ttpt) cc_final: 0.7932 (mmtm)
REVERT: K  340 LYS cc_start: 0.7929 (mttm) cc_final: 0.7603 (mptt)
REVERT: K  372 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7077 (tm-30)
REVERT: L  340 LYS cc_start: 0.8626 (tttt) cc_final: 0.8367 (mttp)
  outliers start: 22
  outliers final: 19
  residues processed: 168
  average time/residue: 0.1107
  time to fit residues: 23.3599
Evaluate side-chains
  176 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 154
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  372 GLU
Chi-restraints excluded: chain F residue  373 THR
Chi-restraints excluded: chain G residue  356 SER
Chi-restraints excluded: chain G residue  371 ILE
Chi-restraints excluded: chain I residue  325 LEU
Chi-restraints excluded: chain I residue  336 GLN
Chi-restraints excluded: chain I residue  337 VAL
Chi-restraints excluded: chain I residue  354 ILE
Chi-restraints excluded: chain I residue  356 SER
Chi-restraints excluded: chain I residue  373 THR
Chi-restraints excluded: chain J residue  324 SER
Chi-restraints excluded: chain J residue  325 LEU
Chi-restraints excluded: chain K residue  325 LEU
Chi-restraints excluded: chain L residue  316 SER
Chi-restraints excluded: chain L residue  324 SER
Chi-restraints excluded: chain L residue  356 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 77 optimal weight:    0.0040
   chunk 59 optimal weight:    5.9990
   chunk 10 optimal weight:    8.9990
   chunk 60 optimal weight:    9.9990
   chunk 14 optimal weight:    4.9990
   chunk 23 optimal weight:   10.0000
   chunk 4 optimal weight:   20.0000
   chunk 75 optimal weight:    8.9990
   chunk 42 optimal weight:   30.0000
   chunk 20 optimal weight:   40.0000
   overall best weight:    5.2000

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

Flipped N/Q/H residues before XYZ refinement:
B 330 HIS
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 307 GLN
H 330 HIS
I 359 ASN
** I 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 307 GLN
K 329 HIS
L 307 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4778 r_free = 0.4778 target = 0.225807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.153159 restraints weight = 7081.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.4198 rms_B_bonded: 1.77
r_work: 0.4098 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.4003 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.4003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.5780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   6996  Z= 0.234
  Angle     :  0.695   6.167   9360  Z= 0.357
  Chirality :  0.050   0.155   1056
  Planarity :  0.004   0.041   1188
  Dihedral  :  5.357  16.870    924
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 16.41 %
    Favored  : 80.18 %
  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 are not related in a simple way.
  whole: -2.48 (0.25), residues: 876
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.88 (0.19), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG J 349 
 TYR   0.012   0.002   TYR E 310 
 PHE   0.009   0.001   PHE K 346 
 HIS   0.005   0.001   HIS G 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 ( 6996)
  covalent geometry    : angle       0.69469 ( 9360)
  hydrogen bonds       : bond        0.02621 (  113)
  hydrogen bonds       : angle       6.10863 (  339)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 158
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.7409 (tttt) cc_final: 0.7183 (ttmm)
REVERT: A  369 LYS cc_start: 0.7953 (mttt) cc_final: 0.7669 (mmmt)
REVERT: B  328 ILE cc_start: 0.5239 (OUTLIER) cc_final: 0.4804 (mm)
REVERT: C  375 LYS cc_start: 0.7048 (tttt) cc_final: 0.6489 (tmmt)
REVERT: E  311 LYS cc_start: 0.5886 (mmtm) cc_final: 0.4230 (pttt)
REVERT: G  340 LYS cc_start: 0.7846 (ptmt) cc_final: 0.7251 (tttm)
REVERT: H  317 LYS cc_start: 0.7377 (tttt) cc_final: 0.6577 (tppt)
REVERT: H  328 ILE cc_start: 0.6603 (mm) cc_final: 0.6323 (mt)
REVERT: H  347 LYS cc_start: 0.7490 (tttt) cc_final: 0.7046 (mmtp)
REVERT: H  349 ARG cc_start: 0.6871 (ttm170) cc_final: 0.5414 (mmp-170)
REVERT: I  336 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.6950 (tt0)
REVERT: I  349 ARG cc_start: 0.6615 (ttm170) cc_final: 0.5258 (ptt-90)
REVERT: K  372 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7149 (tm-30)
REVERT: L  340 LYS cc_start: 0.8704 (tttt) cc_final: 0.8380 (mttp)
  outliers start: 27
  outliers final: 19
  residues processed: 170
  average time/residue: 0.1092
  time to fit residues: 23.2088
Evaluate side-chains
  174 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 152
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain E residue  327 ASN
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  373 THR
Chi-restraints excluded: chain G residue  356 SER
Chi-restraints excluded: chain H residue  371 ILE
Chi-restraints excluded: chain I residue  325 LEU
Chi-restraints excluded: chain I residue  336 GLN
Chi-restraints excluded: chain I residue  337 VAL
Chi-restraints excluded: chain I residue  354 ILE
Chi-restraints excluded: chain I residue  356 SER
Chi-restraints excluded: chain I residue  373 THR
Chi-restraints excluded: chain J residue  324 SER
Chi-restraints excluded: chain J residue  325 LEU
Chi-restraints excluded: chain K residue  325 LEU
Chi-restraints excluded: chain K residue  372 GLU
Chi-restraints excluded: chain L residue  324 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 64 optimal weight:   10.0000
   chunk 71 optimal weight:    6.9990
   chunk 66 optimal weight:    7.9990
   chunk 22 optimal weight:    8.9990
   chunk 21 optimal weight:    5.9990
   chunk 36 optimal weight:   20.0000
   chunk 9 optimal weight:    1.9990
   chunk 20 optimal weight:   20.0000
   chunk 58 optimal weight:   10.0000
   chunk 76 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
C 307 GLN
I 359 ASN
** I 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 307 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4849 r_free = 0.4849 target = 0.230644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.158386 restraints weight = 7309.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.4248 rms_B_bonded: 1.88
r_work: 0.4147 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.4049 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.4049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.6036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6996  Z= 0.189
  Angle     :  0.650   7.753   9360  Z= 0.335
  Chirality :  0.049   0.150   1056
  Planarity :  0.004   0.040   1188
  Dihedral  :  4.999  17.066    924
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 18.31 %
    Favored  : 78.79 %
  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 are not related in a simple way.
  whole: -2.55 (0.25), residues: 876
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.94 (0.19), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG J 349 
 TYR   0.011   0.002   TYR E 310 
 PHE   0.006   0.001   PHE D 378 
 HIS   0.004   0.001   HIS G 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 6996)
  covalent geometry    : angle       0.64961 ( 9360)
  hydrogen bonds       : bond        0.02415 (  113)
  hydrogen bonds       : angle       5.91754 (  339)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 155
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A  369 LYS cc_start: 0.7922 (mttt) cc_final: 0.7679 (mmmt)
REVERT: B  328 ILE cc_start: 0.5294 (OUTLIER) cc_final: 0.4821 (mm)
REVERT: C  311 LYS cc_start: 0.8029 (tttt) cc_final: 0.7469 (ptpp)
REVERT: C  325 LEU cc_start: 0.4073 (pt) cc_final: 0.3447 (mt)
REVERT: C  375 LYS cc_start: 0.7030 (tttt) cc_final: 0.6489 (tmmt)
REVERT: D  372 GLU cc_start: 0.8289 (tt0) cc_final: 0.8037 (tt0)
REVERT: E  311 LYS cc_start: 0.5862 (mmtm) cc_final: 0.4127 (pttt)
REVERT: G  338 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7481 (mm-30)
REVERT: G  340 LYS cc_start: 0.7850 (ptmt) cc_final: 0.7479 (mttt)
REVERT: G  349 ARG cc_start: 0.7320 (mtp85) cc_final: 0.7112 (mtp85)
REVERT: H  317 LYS cc_start: 0.7419 (tttt) cc_final: 0.6614 (tppt)
REVERT: H  328 ILE cc_start: 0.6648 (mm) cc_final: 0.6367 (mt)
REVERT: H  347 LYS cc_start: 0.7406 (tttt) cc_final: 0.6901 (mmtp)
REVERT: H  349 ARG cc_start: 0.6956 (ttm170) cc_final: 0.5446 (mmp-170)
REVERT: I  336 GLN cc_start: 0.7122 (OUTLIER) cc_final: 0.6659 (tt0)
REVERT: I  349 ARG cc_start: 0.6559 (ttm170) cc_final: 0.5303 (ptt-90)
REVERT: K  372 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7100 (tm-30)
REVERT: L  340 LYS cc_start: 0.8683 (tttt) cc_final: 0.8441 (mttp)
  outliers start: 23
  outliers final: 17
  residues processed: 167
  average time/residue: 0.1133
  time to fit residues: 23.5367
Evaluate side-chains
  173 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 153
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain E residue  327 ASN
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  373 THR
Chi-restraints excluded: chain G residue  356 SER
Chi-restraints excluded: chain I residue  325 LEU
Chi-restraints excluded: chain I residue  336 GLN
Chi-restraints excluded: chain I residue  337 VAL
Chi-restraints excluded: chain I residue  339 VAL
Chi-restraints excluded: chain I residue  356 SER
Chi-restraints excluded: chain I residue  373 THR
Chi-restraints excluded: chain J residue  324 SER
Chi-restraints excluded: chain J residue  325 LEU
Chi-restraints excluded: chain K residue  325 LEU
Chi-restraints excluded: chain K residue  372 GLU
Chi-restraints excluded: chain L residue  324 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 11 optimal weight:    0.3980
   chunk 77 optimal weight:    6.9990
   chunk 59 optimal weight:    0.0770
   chunk 61 optimal weight:    8.9990
   chunk 12 optimal weight:    8.9990
   chunk 22 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   chunk 62 optimal weight:    0.0870
   chunk 51 optimal weight:   20.0000
   chunk 57 optimal weight:   10.0000
   overall best weight:    2.7120

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

Flipped N/Q/H residues before XYZ refinement:
C 307 GLN
** I 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 307 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4843 r_free = 0.4843 target = 0.241272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.165073 restraints weight = 7347.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.4266 rms_B_bonded: 1.80
r_work: 0.4176 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.4081 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.4081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.6195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6996  Z= 0.145
  Angle     :  0.616   7.135   9360  Z= 0.317
  Chirality :  0.048   0.144   1056
  Planarity :  0.004   0.038   1188
  Dihedral  :  4.733  15.810    924
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 18.56 %
    Favored  : 78.41 %
  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 are not related in a simple way.
  whole: -2.54 (0.25), residues: 876
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.93 (0.19), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H 379 
 TYR   0.009   0.001   TYR E 310 
 PHE   0.005   0.001   PHE D 378 
 HIS   0.004   0.001   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 6996)
  covalent geometry    : angle       0.61632 ( 9360)
  hydrogen bonds       : bond        0.02130 (  113)
  hydrogen bonds       : angle       5.71629 (  339)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 165
  time to evaluate  : 0.293 
Fit side-chains
REVERT: A  369 LYS cc_start: 0.7996 (mttt) cc_final: 0.7727 (mmmt)
REVERT: B  328 ILE cc_start: 0.5202 (OUTLIER) cc_final: 0.4676 (mm)
REVERT: C  311 LYS cc_start: 0.8003 (tttt) cc_final: 0.7447 (ptpp)
REVERT: C  321 LYS cc_start: 0.6877 (ptpt) cc_final: 0.6301 (ttmm)
REVERT: C  325 LEU cc_start: 0.3950 (pt) cc_final: 0.3323 (mt)
REVERT: C  375 LYS cc_start: 0.7116 (tttt) cc_final: 0.6557 (tmmt)
REVERT: D  353 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8038 (tttm)
REVERT: D  372 GLU cc_start: 0.8179 (tt0) cc_final: 0.7899 (tt0)
REVERT: E  311 LYS cc_start: 0.5808 (mmtm) cc_final: 0.4121 (pttt)
REVERT: G  338 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7523 (mm-30)
REVERT: G  340 LYS cc_start: 0.7769 (ptmt) cc_final: 0.7417 (mttt)
REVERT: G  349 ARG cc_start: 0.7335 (mtp85) cc_final: 0.7072 (mtp85)
REVERT: G  353 LYS cc_start: 0.7244 (tmtt) cc_final: 0.7015 (tmtt)
REVERT: H  317 LYS cc_start: 0.7544 (tttt) cc_final: 0.6744 (tppt)
REVERT: H  328 ILE cc_start: 0.6677 (mm) cc_final: 0.6408 (mt)
REVERT: H  347 LYS cc_start: 0.7402 (tttt) cc_final: 0.6928 (mmtm)
REVERT: H  349 ARG cc_start: 0.6943 (ttm170) cc_final: 0.5426 (mmp-170)
REVERT: I  336 GLN cc_start: 0.7160 (OUTLIER) cc_final: 0.6678 (tt0)
REVERT: I  349 ARG cc_start: 0.6591 (ttm170) cc_final: 0.5306 (ptt-90)
REVERT: I  363 VAL cc_start: 0.8194 (p) cc_final: 0.7958 (t)
REVERT: J  340 LYS cc_start: 0.8236 (mptt) cc_final: 0.7999 (mptt)
REVERT: K  311 LYS cc_start: 0.8644 (ttpt) cc_final: 0.7952 (mmtm)
REVERT: K  349 ARG cc_start: 0.8114 (mtt90) cc_final: 0.6478 (mmp-170)
REVERT: K  372 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7094 (tm-30)
REVERT: L  340 LYS cc_start: 0.8627 (tttt) cc_final: 0.8407 (mttp)
  outliers start: 24
  outliers final: 18
  residues processed: 176
  average time/residue: 0.1170
  time to fit residues: 25.4278
Evaluate side-chains
  182 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 160
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain C residue  307 GLN
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain D residue  353 LYS
Chi-restraints excluded: chain E residue  327 ASN
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  373 THR
Chi-restraints excluded: chain G residue  339 VAL
Chi-restraints excluded: chain G residue  356 SER
Chi-restraints excluded: chain I residue  325 LEU
Chi-restraints excluded: chain I residue  336 GLN
Chi-restraints excluded: chain I residue  337 VAL
Chi-restraints excluded: chain I residue  339 VAL
Chi-restraints excluded: chain I residue  356 SER
Chi-restraints excluded: chain I residue  373 THR
Chi-restraints excluded: chain J residue  324 SER
Chi-restraints excluded: chain J residue  325 LEU
Chi-restraints excluded: chain K residue  325 LEU
Chi-restraints excluded: chain K residue  372 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 45 optimal weight:   40.0000
   chunk 27 optimal weight:    7.9990
   chunk 71 optimal weight:   10.0000
   chunk 46 optimal weight:   30.0000
   chunk 62 optimal weight:    9.9990
   chunk 83 optimal weight:    7.9990
   chunk 36 optimal weight:    1.9990
   chunk 63 optimal weight:   10.0000
   chunk 75 optimal weight:    0.9990
   chunk 31 optimal weight:    8.9990
   chunk 12 optimal weight:   30.0000
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 330 HIS
C 307 GLN
I 359 ASN
** I 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 307 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4839 r_free = 0.4839 target = 0.227622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.154183 restraints weight = 7194.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.4217 rms_B_bonded: 1.89
r_work: 0.4112 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.4012 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.4012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.6274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   6996  Z= 0.248
  Angle     :  0.714   7.333   9360  Z= 0.370
  Chirality :  0.051   0.160   1056
  Planarity :  0.005   0.074   1188
  Dihedral  :  5.081  16.552    924
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.22 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 18.94 %
    Favored  : 78.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.67 (0.25), residues: 876
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.02 (0.19), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG H 379 
 TYR   0.014   0.002   TYR E 310 
 PHE   0.008   0.001   PHE K 346 
 HIS   0.005   0.001   HIS G 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00586 ( 6996)
  covalent geometry    : angle       0.71421 ( 9360)
  hydrogen bonds       : bond        0.02648 (  113)
  hydrogen bonds       : angle       5.98109 (  339)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 159
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
REVERT: A  369 LYS cc_start: 0.7999 (mttt) cc_final: 0.7739 (mmmt)
REVERT: B  328 ILE cc_start: 0.5381 (OUTLIER) cc_final: 0.4923 (mm)
REVERT: C  311 LYS cc_start: 0.7993 (tttt) cc_final: 0.7512 (ptpp)
REVERT: C  321 LYS cc_start: 0.6789 (ptpt) cc_final: 0.6201 (ttmm)
REVERT: C  325 LEU cc_start: 0.3750 (pt) cc_final: 0.3159 (tp)
REVERT: C  375 LYS cc_start: 0.7000 (tttt) cc_final: 0.6426 (tmmt)
REVERT: E  311 LYS cc_start: 0.5760 (mmtm) cc_final: 0.3983 (pttt)
REVERT: G  340 LYS cc_start: 0.7876 (ptmt) cc_final: 0.7519 (mttt)
REVERT: G  349 ARG cc_start: 0.7392 (mtp85) cc_final: 0.7105 (mtp85)
REVERT: H  317 LYS cc_start: 0.7646 (tttt) cc_final: 0.6867 (tppt)
REVERT: H  328 ILE cc_start: 0.6649 (mm) cc_final: 0.6350 (mt)
REVERT: H  347 LYS cc_start: 0.7432 (tttt) cc_final: 0.6933 (mmtm)
REVERT: H  349 ARG cc_start: 0.6957 (ttm170) cc_final: 0.5330 (mmp-170)
REVERT: I  336 GLN cc_start: 0.7206 (OUTLIER) cc_final: 0.6739 (tt0)
REVERT: I  349 ARG cc_start: 0.6590 (ttm170) cc_final: 0.5273 (ptt-90)
REVERT: I  363 VAL cc_start: 0.8187 (p) cc_final: 0.7953 (t)
REVERT: K  372 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7175 (tm-30)
REVERT: L  340 LYS cc_start: 0.8683 (tttt) cc_final: 0.8395 (mttp)
  outliers start: 22
  outliers final: 17
  residues processed: 169
  average time/residue: 0.1148
  time to fit residues: 23.9903
Evaluate side-chains
  178 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 158
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain C residue  307 GLN
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  373 THR
Chi-restraints excluded: chain G residue  339 VAL
Chi-restraints excluded: chain G residue  356 SER
Chi-restraints excluded: chain H residue  360 ILE
Chi-restraints excluded: chain I residue  325 LEU
Chi-restraints excluded: chain I residue  336 GLN
Chi-restraints excluded: chain I residue  337 VAL
Chi-restraints excluded: chain I residue  339 VAL
Chi-restraints excluded: chain I residue  356 SER
Chi-restraints excluded: chain I residue  373 THR
Chi-restraints excluded: chain J residue  324 SER
Chi-restraints excluded: chain J residue  325 LEU
Chi-restraints excluded: chain K residue  372 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 46 optimal weight:   20.0000
   chunk 29 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   chunk 62 optimal weight:    6.9990
   chunk 42 optimal weight:   30.0000
   chunk 57 optimal weight:   30.0000
   chunk 79 optimal weight:    0.9980
   chunk 40 optimal weight:    8.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
C 307 GLN
I 359 ASN
** I 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 307 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4839 r_free = 0.4839 target = 0.230271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.158432 restraints weight = 6988.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.4251 rms_B_bonded: 1.79
r_work: 0.4148 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.4053 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.4053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.6350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6996  Z= 0.137
  Angle     :  0.625   7.218   9360  Z= 0.321
  Chirality :  0.048   0.143   1056
  Planarity :  0.004   0.068   1188
  Dihedral  :  4.755  16.373    924
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.07 %
    Favored  : 78.66 %
  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 are not related in a simple way.
  whole: -2.64 (0.25), residues: 876
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.01 (0.19), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG H 379 
 TYR   0.009   0.001   TYR E 310 
 PHE   0.005   0.001   PHE D 378 
 HIS   0.003   0.001   HIS F 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 6996)
  covalent geometry    : angle       0.62507 ( 9360)
  hydrogen bonds       : bond        0.02160 (  113)
  hydrogen bonds       : angle       5.74775 (  339)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2413.12 seconds
wall clock time: 41 minutes 58.02 seconds (2518.02 seconds total)