Starting phenix.real_space_refine
on Fri Jun  6 02:19:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qjw_14024/06_2025/7qjw_14024.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qjw_14024/06_2025/7qjw_14024.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qjw_14024/06_2025/7qjw_14024.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qjw_14024/06_2025/7qjw_14024.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qjw_14024/06_2025/7qjw_14024.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qjw_14024/06_2025/7qjw_14024.cif"
  }
  resolution = 2.81
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C    2160      2.51       5
     N     636      2.21       5
     O     642      1.98       5
     H    3588      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 7032
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "B"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "C"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "D"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "E"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "F"
      Number of atoms: 1172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1172
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
  Time building chain proxies: 3.98, per 1000 atoms: 0.57
  Number of scatterers: 7032
  At special positions: 0
  Unit cell: (151.725, 105.825, 39.525, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       6     16.00
     O     642      8.00
     N     636      7.00
     C    2160      6.00
     H    3588      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.72
  Conformation dependent library (CDL) restraints added in 650.3 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 14 sheets defined
      0.0% alpha, 49.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310
      removed outlier: 6.549A  pdb=" N   GLN A 307 " --> pdb=" O   ILE E 308 " (cutoff:3.500A)
      removed outlier: 8.096A  pdb=" N   TYR E 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   VAL A 309 " --> pdb=" O   TYR E 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 317 through 322
      removed outlier: 6.466A  pdb=" N   LYS A 317 " --> pdb=" O   VAL E 318 " (cutoff:3.500A)
      removed outlier: 8.438A  pdb=" N   SER E 320 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   THR A 319 " --> pdb=" O   SER E 320 " (cutoff:3.500A)
      removed outlier: 8.685A  pdb=" N   CYS E 322 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   LYS A 321 " --> pdb=" O   CYS E 322 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 325 through 330
      removed outlier: 6.099A  pdb=" N   GLY A 326 " --> pdb=" O   ASN C 327 " (cutoff:3.500A)
      removed outlier: 8.640A  pdb=" N   HIS C 329 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   ILE A 328 " --> pdb=" O   HIS C 329 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   GLY E 326 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   ASN A 327 " --> pdb=" O   GLY E 326 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 337 through 346
      removed outlier: 6.877A  pdb=" N   GLU A 338 " --> pdb=" O   VAL C 337 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   VAL C 339 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   LYS A 340 " --> pdb=" O   VAL C 339 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   SER C 341 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   GLU A 342 " --> pdb=" O   SER C 341 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   LYS C 343 " --> pdb=" O   GLU A 342 " (cutoff:3.500A)
      removed outlier: 9.129A  pdb=" N   VAL A 337 " --> pdb=" O   GLU E 338 " (cutoff:3.500A)
      removed outlier: 10.376A  pdb=" N   LYS E 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 9.026A  pdb=" N   VAL A 339 " --> pdb=" O   LYS E 340 " (cutoff:3.500A)
      removed outlier: 10.473A  pdb=" N   GLU E 342 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 9.236A  pdb=" N   SER A 341 " --> pdb=" O   GLU E 342 " (cutoff:3.500A)
      removed outlier: 9.666A  pdb=" N   LEU E 344 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   LYS A 343 " --> pdb=" O   LEU E 344 " (cutoff:3.500A)
      removed outlier: 8.223A  pdb=" N   PHE E 346 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   ASP A 345 " --> pdb=" O   PHE E 346 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 350 through 357
      removed outlier: 6.778A  pdb=" N   GLN A 351 " --> pdb=" O   SER E 352 " (cutoff:3.500A)
      removed outlier: 8.346A  pdb=" N   ILE E 354 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   LYS A 353 " --> pdb=" O   ILE E 354 " (cutoff:3.500A)
      removed outlier: 7.400A  pdb=" N   SER E 356 " --> pdb=" O   LYS A 353 " (cutoff:3.500A)
      removed outlier: 6.099A  pdb=" N   GLY A 355 " --> pdb=" O   SER E 356 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 360 through 362
      removed outlier: 6.608A  pdb=" N   THR A 361 " --> pdb=" O   HIS C 362 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 369 through 374
      removed outlier: 6.702A  pdb=" N   LYS A 369 " --> pdb=" O   LYS E 370 " (cutoff:3.500A)
      removed outlier: 8.369A  pdb=" N   GLU E 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   ILE A 371 " --> pdb=" O   GLU E 372 " (cutoff:3.500A)
      removed outlier: 8.331A  pdb=" N   HIS E 374 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   THR A 373 " --> pdb=" O   HIS E 374 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 306 through 310
      removed outlier: 6.446A  pdb=" N   GLN B 307 " --> pdb=" O   ILE F 308 " (cutoff:3.500A)
      removed outlier: 7.838A  pdb=" N   TYR F 310 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   VAL B 309 " --> pdb=" O   TYR F 310 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 317 through 322
      removed outlier: 6.527A  pdb=" N   LYS B 317 " --> pdb=" O   VAL F 318 " (cutoff:3.500A)
      removed outlier: 8.372A  pdb=" N   SER F 320 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   THR B 319 " --> pdb=" O   SER F 320 " (cutoff:3.500A)
      removed outlier: 8.656A  pdb=" N   CYS F 322 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   LYS B 321 " --> pdb=" O   CYS F 322 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 325 through 330
      removed outlier: 6.098A  pdb=" N   GLY B 326 " --> pdb=" O   ASN D 327 " (cutoff:3.500A)
      removed outlier: 8.660A  pdb=" N   HIS D 329 " --> pdb=" O   GLY B 326 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   ILE B 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   GLY F 326 " --> pdb=" O   LEU B 325 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   ASN B 327 " --> pdb=" O   GLY F 326 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 337 through 346
      removed outlier: 6.862A  pdb=" N   GLU B 338 " --> pdb=" O   VAL D 337 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   VAL D 339 " --> pdb=" O   GLU B 338 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   LYS B 340 " --> pdb=" O   VAL D 339 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   SER D 341 " --> pdb=" O   LYS B 340 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   GLU B 342 " --> pdb=" O   SER D 341 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   LYS D 343 " --> pdb=" O   GLU B 342 " (cutoff:3.500A)
      removed outlier: 9.120A  pdb=" N   VAL B 337 " --> pdb=" O   GLU F 338 " (cutoff:3.500A)
      removed outlier: 10.396A  pdb=" N   LYS F 340 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 9.019A  pdb=" N   VAL B 339 " --> pdb=" O   LYS F 340 " (cutoff:3.500A)
      removed outlier: 10.457A  pdb=" N   GLU F 342 " --> pdb=" O   VAL B 339 " (cutoff:3.500A)
      removed outlier: 9.239A  pdb=" N   SER B 341 " --> pdb=" O   GLU F 342 " (cutoff:3.500A)
      removed outlier: 9.625A  pdb=" N   LEU F 344 " --> pdb=" O   SER B 341 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   LYS B 343 " --> pdb=" O   LEU F 344 " (cutoff:3.500A)
      removed outlier: 8.168A  pdb=" N   PHE F 346 " --> pdb=" O   LYS B 343 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   ASP B 345 " --> pdb=" O   PHE F 346 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 350 through 357
      removed outlier: 6.766A  pdb=" N   GLN B 351 " --> pdb=" O   SER F 352 " (cutoff:3.500A)
      removed outlier: 8.357A  pdb=" N   ILE F 354 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   LYS B 353 " --> pdb=" O   ILE F 354 " (cutoff:3.500A)
      removed outlier: 7.476A  pdb=" N   SER F 356 " --> pdb=" O   LYS B 353 " (cutoff:3.500A)
      removed outlier: 6.099A  pdb=" N   GLY B 355 " --> pdb=" O   SER F 356 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 360 through 362
      removed outlier: 6.564A  pdb=" N   THR B 361 " --> pdb=" O   HIS D 362 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 369 through 374
      removed outlier: 6.615A  pdb=" N   LYS B 369 " --> pdb=" O   LYS F 370 " (cutoff:3.500A)
      removed outlier: 8.266A  pdb=" N   GLU F 372 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   ILE B 371 " --> pdb=" O   GLU F 372 " (cutoff:3.500A)
      removed outlier: 8.243A  pdb=" N   HIS F 374 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   THR B 373 " --> pdb=" O   HIS F 374 " (cutoff:3.500A)

    58 hydrogen bonds defined for protein.
    174 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: 2.45

  Time building geometry restraints manager: 2.13 seconds

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

  Histogram of bond lengths:
        0.94 -     1.11: 3582
        1.11 -     1.29: 570
        1.29 -     1.46: 905
        1.46 -     1.64: 2023
        1.64 -     1.81: 6
  Bond restraints: 7086
  Sorted by residual:
  bond pdb=" N   SER F 324 "
       pdb=" H   SER F 324 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" N   LEU A 315 "
       pdb=" H   LEU A 315 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.69e+01
  bond pdb=" NE2 GLN E 307 "
       pdb="HE22 GLN E 307 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.69e+01
  bond pdb=" N   GLY E 365 "
       pdb=" H   GLY E 365 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.69e+01
  bond pdb=" N   ASN F 368 "
       pdb=" H   ASN F 368 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.69e+01
  ... (remaining 7081 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 10392
        2.42 -     4.84: 1954
        4.84 -     7.26: 514
        7.26 -     9.68: 46
        9.68 -    12.10: 6
  Bond angle restraints: 12912
  Sorted by residual:
  angle pdb=" CA  ASP E 345 "
        pdb=" CB  ASP E 345 "
        pdb=" CG  ASP E 345 "
      ideal   model   delta    sigma   weight residual
     112.60  118.22   -5.62 1.00e+00 1.00e+00 3.16e+01
  angle pdb=" CA  ASP F 345 "
        pdb=" CB  ASP F 345 "
        pdb=" CG  ASP F 345 "
      ideal   model   delta    sigma   weight residual
     112.60  118.17   -5.57 1.00e+00 1.00e+00 3.10e+01
  angle pdb=" CA  ASP B 345 "
        pdb=" CB  ASP B 345 "
        pdb=" CG  ASP B 345 "
      ideal   model   delta    sigma   weight residual
     112.60  118.10   -5.50 1.00e+00 1.00e+00 3.03e+01
  angle pdb=" N   GLY B 326 "
        pdb=" CA  GLY B 326 "
        pdb=" C   GLY B 326 "
      ideal   model   delta    sigma   weight residual
     110.42  118.52   -8.10 1.49e+00 4.50e-01 2.95e+01
  angle pdb=" N   GLY A 326 "
        pdb=" CA  GLY A 326 "
        pdb=" C   GLY A 326 "
      ideal   model   delta    sigma   weight residual
     110.75  118.53   -7.78 1.46e+00 4.69e-01 2.84e+01
  ... (remaining 12907 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.36: 2901
       16.36 -    32.71: 172
       32.71 -    49.06: 71
       49.06 -    65.41: 112
       65.41 -    81.76: 8
  Dihedral angle restraints: 3264
    sinusoidal: 1866
      harmonic: 1398
  Sorted by residual:
  dihedral pdb=" CA  THR B 377 "
           pdb=" C   THR B 377 "
           pdb=" N   PHE B 378 "
           pdb=" CA  PHE B 378 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.89  -23.11     0      5.00e+00 4.00e-02 2.14e+01
  dihedral pdb=" CA  VAL F 318 "
           pdb=" C   VAL F 318 "
           pdb=" N   THR F 319 "
           pdb=" CA  THR F 319 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.46  -22.54     0      5.00e+00 4.00e-02 2.03e+01
  dihedral pdb=" CA  THR F 377 "
           pdb=" C   THR F 377 "
           pdb=" N   PHE F 378 "
           pdb=" CA  PHE F 378 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.49  -22.51     0      5.00e+00 4.00e-02 2.03e+01
  ... (remaining 3261 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.068: 275
       0.068 -    0.135: 163
       0.135 -    0.202: 70
       0.202 -    0.269: 16
       0.269 -    0.336: 4
  Chirality restraints: 528
  Sorted by residual:
  chirality pdb=" CA  SER D 316 "
            pdb=" N   SER D 316 "
            pdb=" C   SER D 316 "
            pdb=" CB  SER D 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.82e+00
  chirality pdb=" CA  ASP E 348 "
            pdb=" N   ASP E 348 "
            pdb=" C   ASP E 348 "
            pdb=" CB  ASP E 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.82   -0.31 2.00e-01 2.50e+01 2.40e+00
  chirality pdb=" CA  ASP F 348 "
            pdb=" N   ASP F 348 "
            pdb=" C   ASP F 348 "
            pdb=" CB  ASP F 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.05e+00
  ... (remaining 525 not shown)

  Planarity restraints: 1020
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 310 "   -0.105 2.00e-02 2.50e+03   4.26e-02 5.44e+01
        pdb=" CG  TYR C 310 "    0.049 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 310 "    0.041 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 310 "    0.036 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 310 "    0.030 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 310 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 310 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR C 310 "   -0.058 2.00e-02 2.50e+03
        pdb=" HD1 TYR C 310 "   -0.007 2.00e-02 2.50e+03
        pdb=" HD2 TYR C 310 "    0.028 2.00e-02 2.50e+03
        pdb=" HE1 TYR C 310 "    0.002 2.00e-02 2.50e+03
        pdb=" HE2 TYR C 310 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS D 330 "   -0.077 2.00e-02 2.50e+03   4.65e-02 4.88e+01
        pdb=" CG  HIS D 330 "    0.082 2.00e-02 2.50e+03
        pdb=" ND1 HIS D 330 "    0.046 2.00e-02 2.50e+03
        pdb=" CD2 HIS D 330 "    0.038 2.00e-02 2.50e+03
        pdb=" CE1 HIS D 330 "    0.006 2.00e-02 2.50e+03
        pdb=" NE2 HIS D 330 "   -0.019 2.00e-02 2.50e+03
        pdb=" HD1 HIS D 330 "   -0.004 2.00e-02 2.50e+03
        pdb=" HD2 HIS D 330 "   -0.024 2.00e-02 2.50e+03
        pdb=" HE1 HIS D 330 "   -0.048 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS C 330 "    0.076 2.00e-02 2.50e+03   4.47e-02 4.49e+01
        pdb=" CG  HIS C 330 "   -0.076 2.00e-02 2.50e+03
        pdb=" ND1 HIS C 330 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD2 HIS C 330 "   -0.039 2.00e-02 2.50e+03
        pdb=" CE1 HIS C 330 "   -0.007 2.00e-02 2.50e+03
        pdb=" NE2 HIS C 330 "    0.017 2.00e-02 2.50e+03
        pdb=" HD1 HIS C 330 "   -0.003 2.00e-02 2.50e+03
        pdb=" HD2 HIS C 330 "    0.021 2.00e-02 2.50e+03
        pdb=" HE1 HIS C 330 "    0.050 2.00e-02 2.50e+03
  ... (remaining 1017 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 552
        2.20 -     2.80: 12503
        2.80 -     3.40: 17578
        3.40 -     4.00: 23208
        4.00 -     4.60: 32933
  Nonbonded interactions: 86774
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP D 314 "
            pdb=" HG  SER D 316 "
     model   vdw
     1.602 2.450
  nonbonded pdb=" OD1 ASP C 314 "
            pdb=" HG  SER C 316 "
     model   vdw
     1.613 2.450
  nonbonded pdb=" OD1 ASP F 314 "
            pdb=" HG  SER F 316 "
     model   vdw
     1.675 2.450
  nonbonded pdb=" OE1 GLU E 338 "
            pdb=" HZ2 LYS F 331 "
     model   vdw
     1.704 2.450
  nonbonded pdb=" HZ3 LYS A 331 "
            pdb=" OE1 GLU F 338 "
     model   vdw
     1.704 2.450
  ... (remaining 86769 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.940
  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:             0.120
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.080
  Process input model:                     19.550
  Find NCS groups from input model:        0.180
  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:             0.010
  Load rotamer database and sin/cos tables:14.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7091
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   0.036   3498  Z= 0.765
  Angle     :  2.090   8.096   4680  Z= 1.385
  Chirality :  0.099   0.336    528
  Planarity :  0.012   0.063    594
  Dihedral  : 11.960  81.758   1344
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  1.37 %
    Allowed  :  2.28 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.35), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.90 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.012   0.004   HIS F 330 
 PHE   0.044   0.017   PHE E 378 
 TYR   0.099   0.033   TYR C 310 
 ARG   0.004   0.001   ARG F 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14075 (   58)
  hydrogen bonds       : angle       7.51539 (  174)
  covalent geometry    : bond        0.01166 ( 3498)
  covalent geometry    : angle       2.09023 ( 4680)

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  348 ASP cc_start: 0.7612 (t0) cc_final: 0.7132 (t0)
REVERT: A  369 LYS cc_start: 0.7512 (tttt) cc_final: 0.7019 (ttmt)
REVERT: A  375 LYS cc_start: 0.6596 (tttt) cc_final: 0.6389 (ttmt)
REVERT: B  369 LYS cc_start: 0.7713 (tttt) cc_final: 0.7034 (ttmt)
REVERT: B  375 LYS cc_start: 0.5730 (tttt) cc_final: 0.5442 (ttmt)
REVERT: C  311 LYS cc_start: 0.7058 (mtmt) cc_final: 0.6788 (tttt)
REVERT: E  340 LYS cc_start: 0.7910 (mtpt) cc_final: 0.7637 (mttt)
REVERT: E  343 LYS cc_start: 0.8097 (mttt) cc_final: 0.6825 (pptt)
REVERT: E  347 LYS cc_start: 0.8209 (mttt) cc_final: 0.6612 (pmtt)
REVERT: E  351 GLN cc_start: 0.8076 (mt0) cc_final: 0.7764 (mt0)
REVERT: E  369 LYS cc_start: 0.8649 (tttt) cc_final: 0.8104 (ttmt)
REVERT: F  343 LYS cc_start: 0.8184 (mttt) cc_final: 0.6870 (pptt)
REVERT: F  347 LYS cc_start: 0.8236 (mttt) cc_final: 0.6671 (pptt)
REVERT: F  369 LYS cc_start: 0.8418 (tttt) cc_final: 0.7983 (ttmt)
REVERT: F  375 LYS cc_start: 0.7555 (tttt) cc_final: 0.7073 (ttmt)
REVERT: F  378 PHE cc_start: 0.5563 (t80) cc_final: 0.5301 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 1.9224
  time to fit residues: 137.7626
Evaluate side-chains
  42 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 20 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    1.5988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4857 r_free = 0.4857 target = 0.207307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4598 r_free = 0.4598 target = 0.182862 restraints weight = 12422.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.4581 rms_B_bonded: 2.04
r_work: 0.4491 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.4404 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.4404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.2564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3498  Z= 0.128
  Angle     :  0.631   3.665   4680  Z= 0.340
  Chirality :  0.051   0.137    528
  Planarity :  0.003   0.020    594
  Dihedral  :  6.427  16.852    462
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.32), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.34 (0.24), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 374 
 PHE   0.028   0.002   PHE A 378 
 TYR   0.013   0.003   TYR C 310 
 ARG   0.002   0.000   ARG A 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02808 (   58)
  hydrogen bonds       : angle       5.16180 (  174)
  covalent geometry    : bond        0.00272 ( 3498)
  covalent geometry    : angle       0.63116 ( 4680)

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
REVERT: A  347 LYS cc_start: 0.8273 (mttt) cc_final: 0.8065 (mtpt)
REVERT: A  369 LYS cc_start: 0.8073 (tttt) cc_final: 0.7810 (ttmt)
REVERT: B  369 LYS cc_start: 0.8220 (tttt) cc_final: 0.7785 (ttmm)
REVERT: C  375 LYS cc_start: 0.7908 (tttt) cc_final: 0.7597 (ttmt)
REVERT: E  343 LYS cc_start: 0.7772 (mttt) cc_final: 0.6843 (pptt)
REVERT: E  372 GLU cc_start: 0.8142 (tt0) cc_final: 0.7844 (mt-10)
REVERT: F  343 LYS cc_start: 0.7767 (mttt) cc_final: 0.6471 (pptt)
REVERT: F  369 LYS cc_start: 0.8210 (tttt) cc_final: 0.7962 (ttmt)
REVERT: F  375 LYS cc_start: 0.8130 (tttt) cc_final: 0.7580 (ttmt)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 2.2286
  time to fit residues: 103.9418
Evaluate side-chains
  40 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 1 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 12 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   overall best weight:    2.2786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4857 r_free = 0.4857 target = 0.207615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4591 r_free = 0.4591 target = 0.182361 restraints weight = 12457.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.4574 rms_B_bonded: 2.07
r_work: 0.4482 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.4395 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.4395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.3276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   3498  Z= 0.127
  Angle     :  0.605   5.845   4680  Z= 0.324
  Chirality :  0.052   0.142    528
  Planarity :  0.005   0.032    594
  Dihedral  :  5.602  15.399    462
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  7.58 %
    Favored  : 91.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.31), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.49 (0.23), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 330 
 PHE   0.022   0.002   PHE A 378 
 TYR   0.018   0.003   TYR C 310 
 ARG   0.002   0.000   ARG B 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02487 (   58)
  hydrogen bonds       : angle       4.74211 (  174)
  covalent geometry    : bond        0.00281 ( 3498)
  covalent geometry    : angle       0.60522 ( 4680)

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.641 
Fit side-chains
   revert: symmetry clash
REVERT: A  369 LYS cc_start: 0.8149 (tttt) cc_final: 0.7912 (ttmt)
REVERT: B  311 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7348 (mttt)
REVERT: B  369 LYS cc_start: 0.8228 (tttt) cc_final: 0.7817 (ttmm)
REVERT: C  311 LYS cc_start: 0.8206 (pttt) cc_final: 0.7735 (pttt)
REVERT: C  375 LYS cc_start: 0.7911 (tttt) cc_final: 0.7565 (ttmt)
REVERT: D  311 LYS cc_start: 0.7823 (pttt) cc_final: 0.7526 (mttt)
REVERT: E  343 LYS cc_start: 0.7801 (mttt) cc_final: 0.6817 (pptt)
REVERT: F  343 LYS cc_start: 0.7744 (mttt) cc_final: 0.6336 (pptt)
REVERT: F  375 LYS cc_start: 0.8036 (tttt) cc_final: 0.7671 (ttmt)
  outliers start: 4
  outliers final: 3
  residues processed: 45
  average time/residue: 2.3740
  time to fit residues: 110.4886
Evaluate side-chains
  37 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain F residue  319 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    7.9990
   chunk 37 optimal weight:    5.9990
   chunk 10 optimal weight:    9.9990
   chunk 12 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 14 optimal weight:    7.9990
   chunk 21 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    3.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4826 r_free = 0.4826 target = 0.203852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.178627 restraints weight = 12309.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.4556 rms_B_bonded: 2.05
r_work: 0.4467 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.4378 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.4378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.3772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3498  Z= 0.162
  Angle     :  0.625   5.802   4680  Z= 0.331
  Chirality :  0.052   0.143    528
  Planarity :  0.005   0.039    594
  Dihedral  :  5.529  15.158    462
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 11.11 %
    Favored  : 87.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.15 (0.30), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.63 (0.23), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 330 
 PHE   0.022   0.002   PHE A 378 
 TYR   0.016   0.004   TYR C 310 
 ARG   0.001   0.000   ARG C 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02532 (   58)
  hydrogen bonds       : angle       4.79774 (  174)
  covalent geometry    : bond        0.00367 ( 3498)
  covalent geometry    : angle       0.62514 ( 4680)

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
REVERT: A  369 LYS cc_start: 0.8163 (tttt) cc_final: 0.7941 (ttmt)
REVERT: B  369 LYS cc_start: 0.8308 (tttt) cc_final: 0.7933 (ttmt)
REVERT: C  311 LYS cc_start: 0.8125 (pttt) cc_final: 0.7666 (pttt)
REVERT: C  375 LYS cc_start: 0.7784 (tttt) cc_final: 0.7493 (ttmt)
REVERT: D  311 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7283 (pttt)
REVERT: D  379 ARG cc_start: 0.7195 (mmt-90) cc_final: 0.6909 (mmt-90)
REVERT: E  343 LYS cc_start: 0.7565 (mttt) cc_final: 0.6456 (pptt)
REVERT: F  340 LYS cc_start: 0.7524 (mtpt) cc_final: 0.7297 (mttt)
REVERT: F  343 LYS cc_start: 0.7814 (mttt) cc_final: 0.6417 (pptt)
REVERT: F  372 GLU cc_start: 0.8114 (tt0) cc_final: 0.7812 (mt-10)
REVERT: F  375 LYS cc_start: 0.8192 (tttt) cc_final: 0.7782 (ttmt)
  outliers start: 5
  outliers final: 4
  residues processed: 39
  average time/residue: 2.5221
  time to fit residues: 101.5582
Evaluate side-chains
  43 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain F residue  319 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 21 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 13 optimal weight:    8.9990
   chunk 12 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    2.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4831 r_free = 0.4831 target = 0.204267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4555 r_free = 0.4555 target = 0.178952 restraints weight = 12056.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.4559 rms_B_bonded: 2.04
r_work: 0.4471 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.4383 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.4383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.4000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3498  Z= 0.150
  Angle     :  0.592   5.730   4680  Z= 0.316
  Chirality :  0.052   0.141    528
  Planarity :  0.005   0.043    594
  Dihedral  :  5.356  14.629    462
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 10.35 %
    Favored  : 88.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.17 (0.30), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.65 (0.23), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 330 
 PHE   0.019   0.002   PHE A 378 
 TYR   0.014   0.003   TYR C 310 
 ARG   0.001   0.000   ARG F 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02462 (   58)
  hydrogen bonds       : angle       4.76420 (  174)
  covalent geometry    : bond        0.00337 ( 3498)
  covalent geometry    : angle       0.59219 ( 4680)

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  310 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.7787 (t80)
REVERT: B  369 LYS cc_start: 0.8257 (tttt) cc_final: 0.7855 (ttmt)
REVERT: C  311 LYS cc_start: 0.8227 (pttt) cc_final: 0.7637 (pttt)
REVERT: C  375 LYS cc_start: 0.7889 (tttt) cc_final: 0.7464 (ttmt)
REVERT: D  311 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7266 (pttt)
REVERT: D  379 ARG cc_start: 0.7267 (mmt-90) cc_final: 0.7052 (tpp-160)
REVERT: E  311 LYS cc_start: 0.8120 (ttpt) cc_final: 0.7837 (mttm)
REVERT: E  343 LYS cc_start: 0.7590 (mttt) cc_final: 0.6566 (pptt)
REVERT: E  349 ARG cc_start: 0.6398 (mtt180) cc_final: 0.4648 (pmt-80)
REVERT: F  343 LYS cc_start: 0.7820 (mttt) cc_final: 0.6365 (pptt)
REVERT: F  375 LYS cc_start: 0.8119 (tttt) cc_final: 0.7754 (ttmt)
  outliers start: 6
  outliers final: 4
  residues processed: 41
  average time/residue: 2.5252
  time to fit residues: 106.8058
Evaluate side-chains
  43 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  310 TYR
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain F residue  319 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 25 optimal weight:    6.9990
   chunk 6 optimal weight:    7.9990
   chunk 21 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 4 optimal weight:    6.9990
   chunk 23 optimal weight:    7.9990
   chunk 15 optimal weight:    3.9990
   chunk 8 optimal weight:    8.9990
   chunk 37 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0020
   overall best weight:    2.7996

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4833 r_free = 0.4833 target = 0.204381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4560 r_free = 0.4560 target = 0.178978 restraints weight = 12111.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.4563 rms_B_bonded: 2.05
r_work: 0.4475 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.4390 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.4390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.4159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3498  Z= 0.142
  Angle     :  0.579   5.552   4680  Z= 0.307
  Chirality :  0.051   0.137    528
  Planarity :  0.005   0.046    594
  Dihedral  :  5.293  14.073    462
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 11.87 %
    Favored  : 86.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.16 (0.31), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.64 (0.23), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 330 
 PHE   0.021   0.002   PHE A 378 
 TYR   0.013   0.003   TYR C 310 
 ARG   0.001   0.000   ARG B 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02307 (   58)
  hydrogen bonds       : angle       4.71478 (  174)
  covalent geometry    : bond        0.00318 ( 3498)
  covalent geometry    : angle       0.57885 ( 4680)

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  369 LYS cc_start: 0.8249 (tttt) cc_final: 0.7853 (ttmm)
REVERT: C  311 LYS cc_start: 0.8108 (pttt) cc_final: 0.7730 (pptt)
REVERT: D  311 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7248 (pttt)
REVERT: D  345 ASP cc_start: 0.8082 (m-30) cc_final: 0.7644 (t0)
REVERT: E  311 LYS cc_start: 0.8135 (ttpt) cc_final: 0.7825 (mttm)
REVERT: E  343 LYS cc_start: 0.7672 (mttt) cc_final: 0.6662 (pptt)
REVERT: E  349 ARG cc_start: 0.6443 (mtt180) cc_final: 0.4713 (pmt-80)
REVERT: F  343 LYS cc_start: 0.7816 (mttt) cc_final: 0.6360 (pptt)
REVERT: F  372 GLU cc_start: 0.7988 (tt0) cc_final: 0.7687 (mt-10)
REVERT: F  375 LYS cc_start: 0.8072 (tttt) cc_final: 0.7695 (ttmt)
  outliers start: 5
  outliers final: 4
  residues processed: 36
  average time/residue: 2.4722
  time to fit residues: 92.1066
Evaluate side-chains
  37 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain F residue  319 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 15 optimal weight:    7.9990
   chunk 6 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9980
   chunk 29 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    3.3988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4827 r_free = 0.4827 target = 0.203902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.178315 restraints weight = 12003.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.4551 rms_B_bonded: 2.03
r_work: 0.4466 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.4379 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.4379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.4278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   3498  Z= 0.169
  Angle     :  0.612   6.161   4680  Z= 0.326
  Chirality :  0.052   0.138    528
  Planarity :  0.005   0.048    594
  Dihedral  :  5.339  14.199    462
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 12.88 %
    Favored  : 85.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.20 (0.31), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.67 (0.24), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 330 
 PHE   0.016   0.002   PHE E 378 
 TYR   0.015   0.003   TYR E 310 
 ARG   0.001   0.000   ARG E 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02488 (   58)
  hydrogen bonds       : angle       4.79027 (  174)
  covalent geometry    : bond        0.00382 ( 3498)
  covalent geometry    : angle       0.61187 ( 4680)

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  369 LYS cc_start: 0.8259 (tttt) cc_final: 0.7879 (ttmm)
REVERT: C  311 LYS cc_start: 0.8203 (pttt) cc_final: 0.7814 (pptt)
REVERT: D  311 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7251 (pttt)
REVERT: D  345 ASP cc_start: 0.8128 (m-30) cc_final: 0.7756 (t0)
REVERT: E  311 LYS cc_start: 0.8174 (ttpt) cc_final: 0.7868 (mttm)
REVERT: E  343 LYS cc_start: 0.7722 (mttt) cc_final: 0.6683 (pptt)
REVERT: E  349 ARG cc_start: 0.6517 (mtt180) cc_final: 0.4729 (pmt-80)
REVERT: E  369 LYS cc_start: 0.8500 (tttt) cc_final: 0.8272 (ttpt)
REVERT: F  340 LYS cc_start: 0.7604 (mtpt) cc_final: 0.7353 (mttt)
REVERT: F  343 LYS cc_start: 0.7429 (mttt) cc_final: 0.6429 (pptt)
REVERT: F  372 GLU cc_start: 0.8026 (tt0) cc_final: 0.7700 (mt-10)
REVERT: F  375 LYS cc_start: 0.8116 (tttt) cc_final: 0.7693 (ttmt)
  outliers start: 5
  outliers final: 4
  residues processed: 36
  average time/residue: 2.5122
  time to fit residues: 93.5306
Evaluate side-chains
  41 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain F residue  319 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:    0.0020
   chunk 38 optimal weight:    3.9990
   chunk 15 optimal weight:    7.9990
   chunk 29 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0060
   chunk 33 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 17 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    0.9608

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4876 r_free = 0.4876 target = 0.209042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.183657 restraints weight = 11987.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.4612 rms_B_bonded: 2.06
r_work: 0.4524 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.4437 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.4437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.4456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3498  Z= 0.078
  Angle     :  0.488   5.201   4680  Z= 0.257
  Chirality :  0.051   0.129    528
  Planarity :  0.005   0.049    594
  Dihedral  :  4.836  13.185    462
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 13.89 %
    Favored  : 85.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.96 (0.32), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.48 (0.24), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS F 330 
 PHE   0.023   0.002   PHE A 378 
 TYR   0.007   0.001   TYR C 310 
 ARG   0.001   0.000   ARG B 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01716 (   58)
  hydrogen bonds       : angle       4.33804 (  174)
  covalent geometry    : bond        0.00178 ( 3498)
  covalent geometry    : angle       0.48788 ( 4680)

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  369 LYS cc_start: 0.8185 (tttt) cc_final: 0.7793 (ttmm)
REVERT: B  379 ARG cc_start: 0.7160 (mmt-90) cc_final: 0.6651 (tpp-160)
REVERT: C  311 LYS cc_start: 0.7985 (pttt) cc_final: 0.7677 (pptt)
REVERT: D  311 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7128 (pttt)
REVERT: D  345 ASP cc_start: 0.8030 (m-30) cc_final: 0.7624 (t0)
REVERT: E  343 LYS cc_start: 0.7666 (mttt) cc_final: 0.6643 (pptt)
REVERT: E  347 LYS cc_start: 0.8350 (mttt) cc_final: 0.6684 (pptt)
REVERT: E  349 ARG cc_start: 0.6313 (mtt180) cc_final: 0.4588 (pmt-80)
REVERT: F  343 LYS cc_start: 0.7373 (mttt) cc_final: 0.6402 (pptt)
REVERT: F  372 GLU cc_start: 0.8013 (tt0) cc_final: 0.7724 (mt-10)
  outliers start: 3
  outliers final: 2
  residues processed: 35
  average time/residue: 2.2710
  time to fit residues: 82.4933
Evaluate side-chains
  31 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 28
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain D residue  311 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 25 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 40 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 15 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4882 r_free = 0.4882 target = 0.209971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4617 r_free = 0.4617 target = 0.185080 restraints weight = 12007.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.4622 rms_B_bonded: 2.06
r_work: 0.4534 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.4449 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.4449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.4587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3498  Z= 0.076
  Angle     :  0.479   4.998   4680  Z= 0.250
  Chirality :  0.051   0.130    528
  Planarity :  0.005   0.050    594
  Dihedral  :  4.527  12.842    462
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 3.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 15.15 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.33), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.35 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS E 362 
 PHE   0.019   0.001   PHE A 378 
 TYR   0.006   0.001   TYR C 310 
 ARG   0.001   0.000   ARG B 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01610 (   58)
  hydrogen bonds       : angle       4.13813 (  174)
  covalent geometry    : bond        0.00178 ( 3498)
  covalent geometry    : angle       0.47882 ( 4680)

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 29
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  369 LYS cc_start: 0.8242 (tttt) cc_final: 0.7825 (ttmm)
REVERT: B  379 ARG cc_start: 0.7218 (mmt-90) cc_final: 0.6838 (mmt-90)
REVERT: C  311 LYS cc_start: 0.7971 (pttt) cc_final: 0.7590 (pptt)
REVERT: C  345 ASP cc_start: 0.7668 (m-30) cc_final: 0.7439 (t0)
REVERT: C  372 GLU cc_start: 0.8070 (tt0) cc_final: 0.7539 (mt-10)
REVERT: D  311 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.6987 (pttt)
REVERT: D  345 ASP cc_start: 0.7946 (m-30) cc_final: 0.7536 (t0)
REVERT: E  343 LYS cc_start: 0.7619 (mttt) cc_final: 0.6614 (pptt)
REVERT: E  347 LYS cc_start: 0.8336 (mttt) cc_final: 0.6675 (pptt)
REVERT: E  349 ARG cc_start: 0.6332 (mtt180) cc_final: 0.4582 (pmt-80)
REVERT: F  343 LYS cc_start: 0.7342 (mttt) cc_final: 0.6379 (pptt)
REVERT: F  372 GLU cc_start: 0.8052 (tt0) cc_final: 0.7744 (mt-10)
  outliers start: 3
  outliers final: 2
  residues processed: 30
  average time/residue: 2.6009
  time to fit residues: 80.7367
Evaluate side-chains
  30 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain D residue  311 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 5 optimal weight:    7.9990
   chunk 41 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 17 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   chunk 6 optimal weight:    8.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.1584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4877 r_free = 0.4877 target = 0.209559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4610 r_free = 0.4610 target = 0.184550 restraints weight = 12229.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.4615 rms_B_bonded: 2.08
r_work: 0.4528 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.4443 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.4443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.4653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3498  Z= 0.078
  Angle     :  0.469   5.017   4680  Z= 0.246
  Chirality :  0.051   0.130    528
  Planarity :  0.005   0.051    594
  Dihedral  :  4.445  12.810    462
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 15.15 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.33), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.27 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS E 362 
 PHE   0.018   0.001   PHE A 378 
 TYR   0.007   0.001   TYR C 310 
 ARG   0.001   0.000   ARG B 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01652 (   58)
  hydrogen bonds       : angle       4.10866 (  174)
  covalent geometry    : bond        0.00178 ( 3498)
  covalent geometry    : angle       0.46860 ( 4680)

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 29
  time to evaluate  : 0.616 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  369 LYS cc_start: 0.8252 (tttt) cc_final: 0.7847 (ttmm)
REVERT: B  379 ARG cc_start: 0.7209 (mmt-90) cc_final: 0.6695 (tpp-160)
REVERT: C  311 LYS cc_start: 0.7936 (pttt) cc_final: 0.7534 (pptt)
REVERT: C  345 ASP cc_start: 0.7676 (m-30) cc_final: 0.7470 (t0)
REVERT: D  311 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.6996 (pttt)
REVERT: D  345 ASP cc_start: 0.7936 (m-30) cc_final: 0.7544 (t0)
REVERT: E  343 LYS cc_start: 0.7607 (mttt) cc_final: 0.6601 (pptt)
REVERT: E  347 LYS cc_start: 0.8383 (mttt) cc_final: 0.6737 (pptt)
REVERT: E  349 ARG cc_start: 0.6392 (mtt180) cc_final: 0.4640 (pmt-80)
REVERT: F  343 LYS cc_start: 0.7354 (mttt) cc_final: 0.6473 (pptt)
REVERT: F  372 GLU cc_start: 0.8023 (tt0) cc_final: 0.7720 (mt-10)
  outliers start: 3
  outliers final: 2
  residues processed: 30
  average time/residue: 2.6609
  time to fit residues: 82.5484
Evaluate side-chains
  31 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 28
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain D residue  311 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 4 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    1.9388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4855 r_free = 0.4855 target = 0.207375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4582 r_free = 0.4582 target = 0.182217 restraints weight = 12088.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.4596 rms_B_bonded: 2.05
r_work: 0.4506 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.4421 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.4421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.4603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3498  Z= 0.104
  Angle     :  0.506   5.073   4680  Z= 0.267
  Chirality :  0.051   0.132    528
  Planarity :  0.005   0.052    594
  Dihedral  :  4.620  13.157    462
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 15.15 %
    Favored  : 83.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.33), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.30 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 330 
 PHE   0.018   0.002   PHE A 378 
 TYR   0.010   0.002   TYR C 310 
 ARG   0.001   0.000   ARG B 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01872 (   58)
  hydrogen bonds       : angle       4.24900 (  174)
  covalent geometry    : bond        0.00238 ( 3498)
  covalent geometry    : angle       0.50608 ( 4680)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5663.27 seconds
wall clock time: 96 minutes 57.14 seconds (5817.14 seconds total)