Starting phenix.real_space_refine
on Wed Feb 12 02:15:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qjw_14024/02_2025/7qjw_14024.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qjw_14024/02_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_14024/02_2025/7qjw_14024.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qjw_14024/02_2025/7qjw_14024.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qjw_14024/02_2025/7qjw_14024.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qjw_14024/02_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.01, 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: 1.62
  Conformation dependent library (CDL) restraints added in 608.2 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: 0.77
  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: 2.25

  Time building geometry restraints manager: 2.03 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:             1.580
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     18.700
  Find NCS groups from input model:        0.170
  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:14.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.800
-------------------------------------------------------------------------------
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= 0.779
  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 

*********************** 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  : 0.601 
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: 1.9938
  time to fit residues: 142.6692
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  : 0.600 
-------------------------------------------------------------------------------
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 = 41)----------------|
| r_work = 0.4598 r_free = 0.4598 target = 0.182858 restraints weight = 12422.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.4581 rms_B_bonded: 2.04
r_work: 0.4491 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.4405 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.4405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
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= 0.187
  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 

*********************** 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  : 0.590 
Fit side-chains
   revert: symmetry clash
REVERT: A  347 LYS cc_start: 0.8273 (mttt) cc_final: 0.8064 (mtpt)
REVERT: A  369 LYS cc_start: 0.8071 (tttt) cc_final: 0.7810 (ttmt)
REVERT: B  369 LYS cc_start: 0.8219 (tttt) cc_final: 0.7784 (ttmm)
REVERT: C  375 LYS cc_start: 0.7907 (tttt) cc_final: 0.7595 (ttmt)
REVERT: E  343 LYS cc_start: 0.7772 (mttt) cc_final: 0.6843 (pptt)
REVERT: E  372 GLU cc_start: 0.8146 (tt0) cc_final: 0.7847 (mt-10)
REVERT: F  343 LYS cc_start: 0.7765 (mttt) cc_final: 0.6470 (pptt)
REVERT: F  369 LYS cc_start: 0.8207 (tttt) cc_final: 0.7960 (ttmt)
REVERT: F  375 LYS cc_start: 0.8132 (tttt) cc_final: 0.7581 (ttmt)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 2.3627
  time to fit residues: 109.9959
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  : 0.628 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 36 optimal weight:    6.9990
   chunk 18 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 10 optimal weight:    6.9990
   overall best weight:    3.7388

-------------------------------------------------------------------------------
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 = 0.4817 r_free = 0.4817 target = 0.202356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.177420 restraints weight = 12376.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.4547 rms_B_bonded: 2.05
r_work: 0.4457 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.4371 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.4371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.3256

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= 0.294
  Angle     :  0.688   6.336   4680  Z= 0.370
  Chirality :  0.053   0.146    528
  Planarity :  0.005   0.037    594
  Dihedral  :  5.898  15.884    462
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  :  7.83 %
    Favored  : 90.91 %
  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: -2.13 (0.30), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.62 (0.23), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C 330 
 PHE   0.025   0.003   PHE A 378 
 TYR   0.023   0.005   TYR C 310 
 ARG   0.002   0.000   ARG B 379 

*********************** 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
  49 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.614 
Fit side-chains
   revert: symmetry clash
REVERT: A  369 LYS cc_start: 0.8186 (tttt) cc_final: 0.7946 (ttmt)
REVERT: B  369 LYS cc_start: 0.8335 (tttt) cc_final: 0.7914 (ttmm)
REVERT: C  311 LYS cc_start: 0.8214 (pttt) cc_final: 0.7809 (pttt)
REVERT: C  347 LYS cc_start: 0.8403 (mttt) cc_final: 0.8191 (mttm)
REVERT: C  370 LYS cc_start: 0.8641 (tttt) cc_final: 0.8428 (tttp)
REVERT: D  311 LYS cc_start: 0.7922 (pttt) cc_final: 0.7633 (mttt)
REVERT: D  347 LYS cc_start: 0.8507 (mttt) cc_final: 0.8224 (mttm)
REVERT: D  348 ASP cc_start: 0.7145 (t0) cc_final: 0.6854 (m-30)
REVERT: E  343 LYS cc_start: 0.7876 (mttt) cc_final: 0.6850 (pptt)
REVERT: F  343 LYS cc_start: 0.7776 (mttt) cc_final: 0.6347 (pptt)
REVERT: F  369 LYS cc_start: 0.8392 (tttt) cc_final: 0.8107 (ttmt)
REVERT: F  375 LYS cc_start: 0.8116 (tttt) cc_final: 0.7726 (ttmt)
  outliers start: 5
  outliers final: 4
  residues processed: 45
  average time/residue: 2.5910
  time to fit residues: 120.3492
Evaluate side-chains
  42 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
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 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:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 10 optimal weight:    8.9990
   chunk 12 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 2 optimal weight:    6.9990
   chunk 14 optimal weight:    2.9990
   chunk 21 optimal weight:    8.9990
   chunk 28 optimal weight:    7.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    2.1988

-------------------------------------------------------------------------------
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 = 0.4844 r_free = 0.4844 target = 0.205634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4575 r_free = 0.4575 target = 0.180476 restraints weight = 12313.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.4580 rms_B_bonded: 2.07
r_work: 0.4493 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.4400 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.4400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.3723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3498  Z= 0.178
  Angle     :  0.554   5.112   4680  Z= 0.294
  Chirality :  0.051   0.137    528
  Planarity :  0.004   0.037    594
  Dihedral  :  5.406  14.863    462
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 10.86 %
    Favored  : 88.38 %
  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: -2.12 (0.30), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.60 (0.23), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F 330 
 PHE   0.019   0.002   PHE A 378 
 TYR   0.012   0.002   TYR C 310 
 ARG   0.002   0.000   ARG F 379 

*********************** 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: 3
    poor density    : 41
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
REVERT: A  369 LYS cc_start: 0.8152 (tttt) cc_final: 0.7931 (ttmt)
REVERT: B  369 LYS cc_start: 0.8219 (tttt) cc_final: 0.7849 (ttmt)
REVERT: C  311 LYS cc_start: 0.8157 (pttt) cc_final: 0.7661 (pttt)
REVERT: C  347 LYS cc_start: 0.8389 (mttt) cc_final: 0.8178 (mttm)
REVERT: C  370 LYS cc_start: 0.8608 (tttt) cc_final: 0.8407 (tttm)
REVERT: D  311 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7291 (pttt)
REVERT: E  343 LYS cc_start: 0.7588 (mttt) cc_final: 0.6567 (pptt)
REVERT: F  343 LYS cc_start: 0.7756 (mttt) cc_final: 0.6357 (pptt)
REVERT: F  369 LYS cc_start: 0.8207 (tttt) cc_final: 0.7958 (ttmt)
REVERT: F  372 GLU cc_start: 0.7950 (tt0) cc_final: 0.7599 (mt-10)
REVERT: F  375 LYS cc_start: 0.8147 (tttt) cc_final: 0.7744 (ttmt)
  outliers start: 3
  outliers final: 2
  residues processed: 41
  average time/residue: 2.4729
  time to fit residues: 104.7330
Evaluate side-chains
  39 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 21 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 13 optimal weight:    8.9990
   chunk 12 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    3.1988

-------------------------------------------------------------------------------
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 = 0.4814 r_free = 0.4814 target = 0.203019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.177507 restraints weight = 12099.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.4548 rms_B_bonded: 2.07
r_work: 0.4457 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.4371 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.4371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.3959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   3498  Z= 0.251
  Angle     :  0.603   5.947   4680  Z= 0.321
  Chirality :  0.052   0.141    528
  Planarity :  0.005   0.040    594
  Dihedral  :  5.396  14.352    462
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 10.35 %
    Favored  : 88.38 %
  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: -2.21 (0.30), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.68 (0.23), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 330 
 PHE   0.019   0.002   PHE A 378 
 TYR   0.016   0.003   TYR C 310 
 ARG   0.001   0.000   ARG E 379 

*********************** 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: 5
    poor density    : 41
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
REVERT: A  369 LYS cc_start: 0.8175 (tttt) cc_final: 0.7957 (ttmt)
REVERT: B  369 LYS cc_start: 0.8299 (tttt) cc_final: 0.7880 (ttmm)
REVERT: C  311 LYS cc_start: 0.8198 (pttt) cc_final: 0.7598 (pttt)
REVERT: C  347 LYS cc_start: 0.8387 (mttt) cc_final: 0.8175 (mttm)
REVERT: D  311 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7252 (pttt)
REVERT: E  311 LYS cc_start: 0.8150 (ttpt) cc_final: 0.7862 (mttm)
REVERT: E  343 LYS cc_start: 0.7679 (mttt) cc_final: 0.6645 (pptt)
REVERT: E  369 LYS cc_start: 0.8543 (tttt) cc_final: 0.8294 (ttpt)
REVERT: F  343 LYS cc_start: 0.7418 (mttt) cc_final: 0.6505 (pptt)
REVERT: F  369 LYS cc_start: 0.8270 (tttt) cc_final: 0.8052 (ttmt)
REVERT: F  375 LYS cc_start: 0.8125 (tttt) cc_final: 0.7763 (ttmt)
  outliers start: 5
  outliers final: 4
  residues processed: 41
  average time/residue: 2.7781
  time to fit residues: 117.2562
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  : 0.587 
-------------------------------------------------------------------------------
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 25 optimal weight:    4.9990
   chunk 6 optimal weight:   10.0000
   chunk 21 optimal weight:    4.9990
   chunk 29 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   chunk 23 optimal weight:    0.1980
   chunk 15 optimal weight:    0.8980
   chunk 8 optimal weight:    8.9990
   chunk 37 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   overall best weight:    3.2186

-------------------------------------------------------------------------------
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 = 0.204156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.178655 restraints weight = 12182.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.4560 rms_B_bonded: 2.06
r_work: 0.4468 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.4381 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.4381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.4114

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= 0.243
  Angle     :  0.593   5.743   4680  Z= 0.315
  Chirality :  0.052   0.137    528
  Planarity :  0.005   0.039    594
  Dihedral  :  5.402  15.940    462
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 11.36 %
    Favored  : 87.37 %
  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: -2.24 (0.31), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.70 (0.23), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 330 
 PHE   0.022   0.002   PHE A 378 
 TYR   0.014   0.003   TYR E 310 
 ARG   0.001   0.000   ARG E 379 

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.590 
Fit side-chains
   revert: symmetry clash
REVERT: B  369 LYS cc_start: 0.8293 (tttt) cc_final: 0.7885 (ttmm)
REVERT: C  311 LYS cc_start: 0.8214 (pttt) cc_final: 0.7828 (pptt)
REVERT: C  347 LYS cc_start: 0.8363 (mttt) cc_final: 0.8143 (mttm)
REVERT: D  311 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7266 (pttt)
REVERT: E  311 LYS cc_start: 0.8160 (ttpt) cc_final: 0.7857 (mttm)
REVERT: E  343 LYS cc_start: 0.7686 (mttt) cc_final: 0.6655 (pptt)
REVERT: E  349 ARG cc_start: 0.6508 (mtt180) cc_final: 0.4748 (pmt-80)
REVERT: E  369 LYS cc_start: 0.8546 (tttt) cc_final: 0.8322 (ttmt)
REVERT: F  343 LYS cc_start: 0.7431 (mttt) cc_final: 0.6505 (pptt)
REVERT: F  369 LYS cc_start: 0.8227 (tttt) cc_final: 0.8021 (ttmt)
REVERT: F  375 LYS cc_start: 0.8091 (tttt) cc_final: 0.7675 (ttmt)
  outliers start: 5
  outliers final: 4
  residues processed: 46
  average time/residue: 2.7519
  time to fit residues: 130.2709
Evaluate side-chains
  47 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
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:    0.1980
   chunk 15 optimal weight:    7.9990
   chunk 6 optimal weight:    8.9990
   chunk 14 optimal weight:    6.9990
   chunk 19 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 11 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 24 optimal weight:    4.9990
   overall best weight:    1.7584

-------------------------------------------------------------------------------
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 = 0.4850 r_free = 0.4850 target = 0.206856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4577 r_free = 0.4577 target = 0.181261 restraints weight = 11903.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.4586 rms_B_bonded: 2.05
r_work: 0.4498 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.4410 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.4410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.4346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3498  Z= 0.156
  Angle     :  0.525   5.261   4680  Z= 0.277
  Chirality :  0.051   0.132    528
  Planarity :  0.005   0.038    594
  Dihedral  :  5.017  13.560    462
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 12.88 %
    Favored  : 86.11 %
  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: -2.03 (0.31), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.54 (0.24), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D 362 
 PHE   0.022   0.002   PHE A 378 
 TYR   0.009   0.002   TYR C 310 
 ARG   0.001   0.000   ARG F 379 

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
REVERT: B  369 LYS cc_start: 0.8229 (tttt) cc_final: 0.7840 (ttmm)
REVERT: C  311 LYS cc_start: 0.8043 (pttt) cc_final: 0.7720 (pptt)
REVERT: C  347 LYS cc_start: 0.8411 (mttt) cc_final: 0.8141 (mttm)
REVERT: D  311 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7155 (pttt)
REVERT: D  345 ASP cc_start: 0.8062 (m-30) cc_final: 0.7654 (t0)
REVERT: E  343 LYS cc_start: 0.7659 (mttt) cc_final: 0.6706 (pptt)
REVERT: E  349 ARG cc_start: 0.6344 (mtt180) cc_final: 0.4593 (pmt-80)
REVERT: F  343 LYS cc_start: 0.7386 (mttt) cc_final: 0.6417 (pptt)
REVERT: F  372 GLU cc_start: 0.7970 (tt0) cc_final: 0.7679 (mt-10)
REVERT: F  375 LYS cc_start: 0.8097 (tttt) cc_final: 0.7711 (ttmt)
  outliers start: 4
  outliers final: 3
  residues processed: 35
  average time/residue: 2.7286
  time to fit residues: 98.5382
Evaluate side-chains
  36 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 32
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:    6.9990
   chunk 38 optimal weight:    0.6980
   chunk 15 optimal weight:    8.9990
   chunk 29 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.6784

-------------------------------------------------------------------------------
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 = 0.4860 r_free = 0.4860 target = 0.207231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4587 r_free = 0.4587 target = 0.181882 restraints weight = 12019.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.4592 rms_B_bonded: 2.07
r_work: 0.4505 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.4418 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.4418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.4498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3498  Z= 0.157
  Angle     :  0.507   5.147   4680  Z= 0.267
  Chirality :  0.051   0.133    528
  Planarity :  0.005   0.043    594
  Dihedral  :  4.856  13.356    462
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 13.38 %
    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: -1.88 (0.32), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.43 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS F 330 
 PHE   0.020   0.002   PHE A 378 
 TYR   0.009   0.002   TYR E 310 
 ARG   0.001   0.000   ARG E 379 

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.622 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  369 LYS cc_start: 0.8198 (tttt) cc_final: 0.7810 (ttmm)
REVERT: C  311 LYS cc_start: 0.8081 (pttt) cc_final: 0.7771 (pptt)
REVERT: C  347 LYS cc_start: 0.8420 (mttt) cc_final: 0.8143 (mttm)
REVERT: D  311 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7103 (pttt)
REVERT: D  345 ASP cc_start: 0.8040 (m-30) cc_final: 0.7674 (t0)
REVERT: E  343 LYS cc_start: 0.7661 (mttt) cc_final: 0.6633 (pptt)
REVERT: E  347 LYS cc_start: 0.8396 (mttt) cc_final: 0.6680 (pptt)
REVERT: E  349 ARG cc_start: 0.6464 (mtt180) cc_final: 0.4724 (pmt-80)
REVERT: F  343 LYS cc_start: 0.7381 (mttt) cc_final: 0.6420 (pptt)
REVERT: F  372 GLU cc_start: 0.7976 (tt0) cc_final: 0.7687 (mt-10)
REVERT: F  375 LYS cc_start: 0.8137 (tttt) cc_final: 0.7887 (ttmp)
  outliers start: 5
  outliers final: 4
  residues processed: 32
  average time/residue: 2.8021
  time to fit residues: 92.7026
Evaluate side-chains
  36 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 25 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 29 optimal weight:    6.9990
   chunk 41 optimal weight:    4.9990
   chunk 15 optimal weight:    8.9990
   chunk 38 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    1.7788

-------------------------------------------------------------------------------
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 = 0.4856 r_free = 0.4856 target = 0.207066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.181855 restraints weight = 12063.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.4591 rms_B_bonded: 2.06
r_work: 0.4500 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.4416 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.4416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.4542

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= 0.158
  Angle     :  0.504   5.102   4680  Z= 0.265
  Chirality :  0.051   0.132    528
  Planarity :  0.005   0.043    594
  Dihedral  :  4.778  13.320    462
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 13.64 %
    Favored  : 85.10 %
  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: -1.83 (0.32), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.39 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS E 374 
 PHE   0.018   0.002   PHE A 378 
 TYR   0.009   0.002   TYR C 310 
 ARG   0.001   0.000   ARG B 379 

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.645 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  369 LYS cc_start: 0.8199 (tttt) cc_final: 0.7840 (ttmm)
REVERT: C  311 LYS cc_start: 0.8075 (pttt) cc_final: 0.7747 (pptt)
REVERT: C  345 ASP cc_start: 0.7753 (m-30) cc_final: 0.7363 (t0)
REVERT: D  311 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7055 (pttt)
REVERT: D  345 ASP cc_start: 0.8049 (m-30) cc_final: 0.7686 (t0)
REVERT: E  343 LYS cc_start: 0.7660 (mttt) cc_final: 0.6633 (pptt)
REVERT: E  347 LYS cc_start: 0.8346 (mttt) cc_final: 0.6671 (pptt)
REVERT: E  349 ARG cc_start: 0.6430 (mtt180) cc_final: 0.4666 (pmt-80)
REVERT: F  343 LYS cc_start: 0.7380 (mttt) cc_final: 0.6422 (pptt)
REVERT: F  372 GLU cc_start: 0.7957 (tt0) cc_final: 0.7692 (mt-10)
REVERT: F  375 LYS cc_start: 0.8142 (tttt) cc_final: 0.7922 (ttmp)
  outliers start: 5
  outliers final: 4
  residues processed: 32
  average time/residue: 2.8997
  time to fit residues: 95.8240
Evaluate side-chains
  35 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 30
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 41 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 6 optimal weight:    7.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4892 r_free = 0.4892 target = 0.210682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.185723 restraints weight = 12212.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.4631 rms_B_bonded: 2.10
r_work: 0.4545 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.4455 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.4455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.4731

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= 0.118
  Angle     :  0.452   5.005   4680  Z= 0.236
  Chirality :  0.050   0.127    528
  Planarity :  0.004   0.044    594
  Dihedral  :  4.405  12.860    462
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 14.65 %
    Favored  : 84.60 %
  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: -1.65 (0.33), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.25 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS E 362 
 PHE   0.017   0.001   PHE A 378 
 TYR   0.005   0.001   TYR C 310 
 ARG   0.000   0.000   ARG E 379 

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 32
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  369 LYS cc_start: 0.8246 (tttt) cc_final: 0.7841 (ttmm)
REVERT: B  379 ARG cc_start: 0.7188 (mmt-90) cc_final: 0.6565 (tpp-160)
REVERT: C  311 LYS cc_start: 0.7947 (pttt) cc_final: 0.7568 (pptt)
REVERT: C  345 ASP cc_start: 0.7692 (m-30) cc_final: 0.7465 (t0)
REVERT: D  311 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.6955 (pttt)
REVERT: D  345 ASP cc_start: 0.7916 (m-30) cc_final: 0.7540 (t0)
REVERT: E  343 LYS cc_start: 0.7596 (mttt) cc_final: 0.6594 (pptt)
REVERT: E  347 LYS cc_start: 0.8374 (mttt) cc_final: 0.6725 (pptt)
REVERT: E  379 ARG cc_start: 0.7143 (mmt-90) cc_final: 0.4316 (ptp90)
REVERT: F  343 LYS cc_start: 0.7400 (mttt) cc_final: 0.6273 (pptt)
REVERT: F  372 GLU cc_start: 0.7972 (tt0) cc_final: 0.7725 (mt-10)
  outliers start: 3
  outliers final: 2
  residues processed: 33
  average time/residue: 2.2981
  time to fit residues: 78.8484
Evaluate side-chains
  29 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 26
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain F residue  319 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 41 optimal weight:    6.9990
   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:    6.9990
   chunk 4 optimal weight:    7.9990
   chunk 8 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    2.1588

-------------------------------------------------------------------------------
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 = 0.4849 r_free = 0.4849 target = 0.206390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.181192 restraints weight = 12158.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.4586 rms_B_bonded: 2.08
r_work: 0.4497 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.4410 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.4410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.4657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3498  Z= 0.178
  Angle     :  0.511   5.086   4680  Z= 0.270
  Chirality :  0.051   0.135    528
  Planarity :  0.005   0.045    594
  Dihedral  :  4.636  13.042    462
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 15.40 %
    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: -1.69 (0.33), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.28 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS E 330 
 PHE   0.017   0.002   PHE A 378 
 TYR   0.011   0.002   TYR C 310 
 ARG   0.001   0.000   ARG B 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5451.86 seconds
wall clock time: 96 minutes 17.71 seconds (5777.71 seconds total)