Starting phenix.real_space_refine
on Tue Mar  3 16:23:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qjw_14024/03_2026/7qjw_14024.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qjw_14024/03_2026/7qjw_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_14024/03_2026/7qjw_14024.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qjw_14024/03_2026/7qjw_14024.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qjw_14024/03_2026/7qjw_14024.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qjw_14024/03_2026/7qjw_14024.cif"
  }
  resolution = 2.81
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.39, per 1000 atoms: 0.20
  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: 0.43
  Conformation dependent library (CDL) restraints added in 314.0 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: 0.16
  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: 1.58

  Time building geometry restraints manager: 0.72 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: 0.00
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:             1.230
  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:             0.040
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.160
  Find NCS groups from input model:        0.090
  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:9.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.900
-------------------------------------------------------------------------------
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 : 0.14
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -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
 ARG   0.004   0.001   ARG F 349 
 TYR   0.099   0.033   TYR C 310 
 PHE   0.044   0.017   PHE E 378 
 HIS   0.012   0.004   HIS F 330 

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

*********************** 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  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  348 ASP cc_start: 0.7611 (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: D  311 LYS cc_start: 0.6561 (mtmt) cc_final: 0.6240 (pttt)
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: 0.9914
  time to fit residues: 70.8111
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  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    1.1988

-------------------------------------------------------------------------------
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 = 0.4868 r_free = 0.4868 target = 0.207967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4601 r_free = 0.4601 target = 0.183195 restraints weight = 12445.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.4587 rms_B_bonded: 2.08
r_work: 0.4499 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.4414 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.4414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.2583

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= 0.126
  Angle     :  0.621   3.639   4680  Z= 0.334
  Chirality :  0.051   0.138    528
  Planarity :  0.003   0.019    594
  Dihedral  :  6.413  16.017    462
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 1.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.73 (0.32), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.31 (0.24), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 349 
 TYR   0.012   0.003   TYR C 310 
 PHE   0.026   0.002   PHE A 378 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 3498)
  covalent geometry    : angle       0.62091 ( 4680)
  hydrogen bonds       : bond        0.02751 (   58)
  hydrogen bonds       : angle       5.12971 (  174)

*********************** 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
  46 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.8277 (mttt) cc_final: 0.8072 (mtpt)
REVERT: A  369 LYS cc_start: 0.8043 (tttt) cc_final: 0.7778 (ttmt)
REVERT: B  347 LYS cc_start: 0.8086 (mttt) cc_final: 0.7494 (mttm)
REVERT: B  369 LYS cc_start: 0.8207 (tttt) cc_final: 0.7746 (ttmm)
REVERT: C  375 LYS cc_start: 0.7976 (tttt) cc_final: 0.7642 (ttmt)
REVERT: E  343 LYS cc_start: 0.7757 (mttt) cc_final: 0.6844 (pptt)
REVERT: E  372 GLU cc_start: 0.8125 (tt0) cc_final: 0.7839 (mt-10)
REVERT: F  343 LYS cc_start: 0.7758 (mttt) cc_final: 0.6478 (pptt)
REVERT: F  369 LYS cc_start: 0.8185 (tttt) cc_final: 0.7942 (ttmt)
REVERT: F  375 LYS cc_start: 0.8116 (tttt) cc_final: 0.7573 (ttmt)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 1.2512
  time to fit residues: 59.1469
Evaluate side-chains
  37 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 6 optimal weight:    8.9990
   chunk 28 optimal weight:    5.9990
   chunk 12 optimal weight:    0.5980
   chunk 22 optimal weight:    9.9990
   chunk 38 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   overall best weight:    1.5184

-------------------------------------------------------------------------------
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 = 0.206403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4602 r_free = 0.4602 target = 0.182422 restraints weight = 12308.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.4600 rms_B_bonded: 2.04
r_work: 0.4506 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.4417 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.4417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.3352

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= 0.102
  Angle     :  0.563   5.772   4680  Z= 0.300
  Chirality :  0.051   0.140    528
  Planarity :  0.004   0.036    594
  Dihedral  :  5.452  14.665    462
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  7.32 %
    Favored  : 91.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.90 (0.30), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.44 (0.23), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 379 
 TYR   0.015   0.003   TYR C 310 
 PHE   0.020   0.002   PHE A 378 
 HIS   0.002   0.001   HIS E 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 3498)
  covalent geometry    : angle       0.56289 ( 4680)
  hydrogen bonds       : bond        0.02264 (   58)
  hydrogen bonds       : angle       4.57659 (  174)

*********************** 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
  47 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
REVERT: A  369 LYS cc_start: 0.8138 (tttt) cc_final: 0.7912 (ttmt)
REVERT: B  311 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7383 (mttt)
REVERT: B  369 LYS cc_start: 0.8222 (tttt) cc_final: 0.7841 (ttmp)
REVERT: C  311 LYS cc_start: 0.8208 (pttt) cc_final: 0.7756 (pttt)
REVERT: C  375 LYS cc_start: 0.7949 (tttt) cc_final: 0.7497 (ttpt)
REVERT: D  311 LYS cc_start: 0.7801 (pttt) cc_final: 0.7511 (mttp)
REVERT: E  343 LYS cc_start: 0.7486 (mttt) cc_final: 0.6501 (pptt)
REVERT: E  372 GLU cc_start: 0.8186 (tt0) cc_final: 0.7906 (mt-10)
REVERT: F  343 LYS cc_start: 0.7694 (mttt) cc_final: 0.6317 (pptt)
REVERT: F  375 LYS cc_start: 0.7981 (tttt) cc_final: 0.7644 (ttmt)
  outliers start: 4
  outliers final: 3
  residues processed: 44
  average time/residue: 1.3079
  time to fit residues: 59.1634
Evaluate side-chains
  38 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
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 21 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 27 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 32 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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 = 0.206242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4574 r_free = 0.4574 target = 0.180789 restraints weight = 12227.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.4576 rms_B_bonded: 2.05
r_work: 0.4490 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.4402 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.4402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
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      :  0.003   0.027   3498  Z= 0.136
  Angle     :  0.586   5.275   4680  Z= 0.310
  Chirality :  0.052   0.141    528
  Planarity :  0.005   0.039    594
  Dihedral  :  5.331  13.892    462
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 10.86 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.05 (0.30), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.55 (0.23), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 379 
 TYR   0.015   0.003   TYR C 310 
 PHE   0.020   0.002   PHE A 378 
 HIS   0.003   0.001   HIS D 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 3498)
  covalent geometry    : angle       0.58607 ( 4680)
  hydrogen bonds       : bond        0.02342 (   58)
  hydrogen bonds       : angle       4.61793 (  174)

*********************** 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
  38 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
REVERT: A  369 LYS cc_start: 0.8292 (tttt) cc_final: 0.7938 (ttmt)
REVERT: B  369 LYS cc_start: 0.8277 (tttt) cc_final: 0.7930 (ttmp)
REVERT: C  311 LYS cc_start: 0.8187 (pttt) cc_final: 0.7735 (pttt)
REVERT: D  311 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7321 (pttt)
REVERT: E  343 LYS cc_start: 0.7535 (mttt) cc_final: 0.6580 (pptt)
REVERT: F  343 LYS cc_start: 0.7790 (mttt) cc_final: 0.6415 (pptt)
REVERT: F  372 GLU cc_start: 0.8078 (tt0) cc_final: 0.7754 (mt-10)
REVERT: F  375 LYS cc_start: 0.8130 (tttt) cc_final: 0.7749 (ttmt)
  outliers start: 4
  outliers final: 3
  residues processed: 34
  average time/residue: 1.1966
  time to fit residues: 41.9301
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  : 0.182 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 32 optimal weight:    6.9990
   chunk 6 optimal weight:    1.9990
   chunk 14 optimal weight:    7.9990
   chunk 33 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    2.3988

-------------------------------------------------------------------------------
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 = 0.4853 r_free = 0.4853 target = 0.206877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.181370 restraints weight = 12134.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.4577 rms_B_bonded: 2.05
r_work: 0.4491 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.4404 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.4404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.3982

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= 0.123
  Angle     :  0.549   5.283   4680  Z= 0.291
  Chirality :  0.051   0.140    528
  Planarity :  0.005   0.042    594
  Dihedral  :  5.134  13.521    462
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 10.61 %
    Favored  : 87.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.00 (0.31), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.51 (0.23), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 379 
 TYR   0.012   0.003   TYR C 310 
 PHE   0.020   0.002   PHE A 378 
 HIS   0.002   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 3498)
  covalent geometry    : angle       0.54904 ( 4680)
  hydrogen bonds       : bond        0.02251 (   58)
  hydrogen bonds       : angle       4.57760 (  174)

*********************** 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
  41 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
REVERT: A  369 LYS cc_start: 0.8277 (tttt) cc_final: 0.7961 (ttmt)
REVERT: B  369 LYS cc_start: 0.8230 (tttt) cc_final: 0.7806 (ttmm)
REVERT: C  311 LYS cc_start: 0.8182 (pttt) cc_final: 0.7598 (pttt)
REVERT: D  311 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7272 (pttt)
REVERT: D  345 ASP cc_start: 0.8016 (m-30) cc_final: 0.7632 (t0)
REVERT: E  343 LYS cc_start: 0.7552 (mttt) cc_final: 0.6600 (pptt)
REVERT: E  349 ARG cc_start: 0.6315 (mtt180) cc_final: 0.4580 (pmt-80)
REVERT: F  343 LYS cc_start: 0.7776 (mttt) cc_final: 0.6454 (pptt)
REVERT: F  372 GLU cc_start: 0.8107 (tt0) cc_final: 0.7782 (mt-10)
REVERT: F  375 LYS cc_start: 0.8085 (tttt) cc_final: 0.7724 (ttmt)
  outliers start: 6
  outliers final: 5
  residues processed: 35
  average time/residue: 1.2280
  time to fit residues: 44.2908
Evaluate side-chains
  37 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
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 D residue  319 THR
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 33 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 39 optimal weight:    0.7980
   chunk 1 optimal weight:    6.9990
   chunk 32 optimal weight:    0.8980
   chunk 28 optimal weight:    8.9990
   chunk 18 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    1.9386

-------------------------------------------------------------------------------
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 = 0.4862 r_free = 0.4862 target = 0.207949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.182266 restraints weight = 12054.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.4590 rms_B_bonded: 2.07
r_work: 0.4500 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.4412 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.4412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.4142

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= 0.108
  Angle     :  0.526   5.100   4680  Z= 0.277
  Chirality :  0.051   0.137    528
  Planarity :  0.005   0.048    594
  Dihedral  :  4.967  13.232    462
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 10.86 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.94 (0.31), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.47 (0.24), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 349 
 TYR   0.011   0.002   TYR C 310 
 PHE   0.016   0.002   PHE A 378 
 HIS   0.002   0.000   HIS A 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 3498)
  covalent geometry    : angle       0.52633 ( 4680)
  hydrogen bonds       : bond        0.02072 (   58)
  hydrogen bonds       : angle       4.45480 (  174)

*********************** 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
  36 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 30
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: A  369 LYS cc_start: 0.8265 (tttt) cc_final: 0.7969 (ttmt)
REVERT: B  369 LYS cc_start: 0.8207 (tttt) cc_final: 0.7798 (ttmm)
REVERT: C  311 LYS cc_start: 0.8111 (pttt) cc_final: 0.7544 (pttt)
REVERT: D  311 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7177 (pttt)
REVERT: D  345 ASP cc_start: 0.8028 (m-30) cc_final: 0.7626 (t0)
REVERT: E  343 LYS cc_start: 0.7523 (mttt) cc_final: 0.6598 (pptt)
REVERT: E  349 ARG cc_start: 0.6296 (mtt180) cc_final: 0.4565 (pmt-80)
REVERT: F  343 LYS cc_start: 0.7791 (mttt) cc_final: 0.6470 (pptt)
REVERT: F  372 GLU cc_start: 0.8084 (tt0) cc_final: 0.7777 (mt-10)
  outliers start: 6
  outliers final: 5
  residues processed: 30
  average time/residue: 1.1580
  time to fit residues: 35.8998
Evaluate side-chains
  33 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 27
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
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 D residue  319 THR
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 37 optimal weight:    2.9990
   chunk 17 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 12 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0670
   chunk 25 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    1.2122

-------------------------------------------------------------------------------
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 = 0.4881 r_free = 0.4881 target = 0.209536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4610 r_free = 0.4610 target = 0.184531 restraints weight = 12039.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.4614 rms_B_bonded: 2.05
r_work: 0.4528 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.4442 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.4442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.4313

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= 0.080
  Angle     :  0.482   5.058   4680  Z= 0.251
  Chirality :  0.051   0.132    528
  Planarity :  0.004   0.047    594
  Dihedral  :  4.641  12.901    462
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.83 (0.32), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.38 (0.24), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 379 
 TYR   0.008   0.001   TYR C 310 
 PHE   0.015   0.001   PHE A 378 
 HIS   0.002   0.000   HIS E 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00179 ( 3498)
  covalent geometry    : angle       0.48170 ( 4680)
  hydrogen bonds       : bond        0.01780 (   58)
  hydrogen bonds       : angle       4.22026 (  174)

*********************** 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
  34 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 29
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  369 LYS cc_start: 0.8222 (tttt) cc_final: 0.7938 (ttmt)
REVERT: B  369 LYS cc_start: 0.8156 (tttt) cc_final: 0.7771 (ttmm)
REVERT: C  311 LYS cc_start: 0.7975 (pttt) cc_final: 0.7465 (pttt)
REVERT: D  345 ASP cc_start: 0.7905 (m-30) cc_final: 0.7533 (t0)
REVERT: E  343 LYS cc_start: 0.7474 (mttt) cc_final: 0.6516 (pptt)
REVERT: E  349 ARG cc_start: 0.6290 (mtt180) cc_final: 0.4585 (pmt-80)
REVERT: F  343 LYS cc_start: 0.7743 (mttt) cc_final: 0.6432 (pptt)
REVERT: F  372 GLU cc_start: 0.7909 (tt0) cc_final: 0.7616 (mt-10)
  outliers start: 5
  outliers final: 4
  residues processed: 30
  average time/residue: 1.2063
  time to fit residues: 37.3065
Evaluate side-chains
  28 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain D residue  319 THR
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 21 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 20 optimal weight:    0.4980
   chunk 18 optimal weight:    7.9990
   chunk 13 optimal weight:    8.9990
   chunk 33 optimal weight:    3.9990
   chunk 36 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    1.6988

-------------------------------------------------------------------------------
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 = 0.4869 r_free = 0.4869 target = 0.208837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4596 r_free = 0.4596 target = 0.183632 restraints weight = 12111.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.4602 rms_B_bonded: 2.06
r_work: 0.4513 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.4425 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.4425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.4362

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= 0.096
  Angle     :  0.499   5.075   4680  Z= 0.262
  Chirality :  0.051   0.136    528
  Planarity :  0.005   0.048    594
  Dihedral  :  4.653  12.890    462
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 12.12 %
    Favored  : 86.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.76 (0.32), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.33 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 349 
 TYR   0.010   0.002   TYR D 310 
 PHE   0.014   0.001   PHE A 378 
 HIS   0.001   0.000   HIS D 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 3498)
  covalent geometry    : angle       0.49870 ( 4680)
  hydrogen bonds       : bond        0.01927 (   58)
  hydrogen bonds       : angle       4.25392 (  174)

*********************** 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
  33 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 28
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  369 LYS cc_start: 0.8231 (tttt) cc_final: 0.7963 (ttmt)
REVERT: B  369 LYS cc_start: 0.8170 (tttt) cc_final: 0.7793 (ttmm)
REVERT: C  311 LYS cc_start: 0.8020 (pttt) cc_final: 0.7518 (pttt)
REVERT: C  345 ASP cc_start: 0.7706 (m-30) cc_final: 0.7459 (t0)
REVERT: D  311 LYS cc_start: 0.7791 (pttt) cc_final: 0.7244 (pttt)
REVERT: D  345 ASP cc_start: 0.7929 (m-30) cc_final: 0.7542 (t0)
REVERT: D  379 ARG cc_start: 0.7342 (mpt180) cc_final: 0.7019 (tpp-160)
REVERT: E  343 LYS cc_start: 0.7549 (mttt) cc_final: 0.6590 (pptt)
REVERT: E  349 ARG cc_start: 0.6322 (mtt180) cc_final: 0.4565 (pmt-80)
REVERT: F  343 LYS cc_start: 0.7782 (mttt) cc_final: 0.6451 (pptt)
REVERT: F  372 GLU cc_start: 0.7913 (tt0) cc_final: 0.7619 (mt-10)
  outliers start: 5
  outliers final: 5
  residues processed: 28
  average time/residue: 1.2226
  time to fit residues: 35.2691
Evaluate side-chains
  32 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 27
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
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  319 THR
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 24 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 11 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 4 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 1 optimal weight:    7.9990
   chunk 19 optimal weight:    0.4980
   chunk 30 optimal weight:    0.9990
   overall best weight:    1.2186

-------------------------------------------------------------------------------
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 = 0.4885 r_free = 0.4885 target = 0.210140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4618 r_free = 0.4618 target = 0.185265 restraints weight = 12034.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.4624 rms_B_bonded: 2.05
r_work: 0.4536 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.4448 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.4448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.4477

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     :  0.464   4.992   4680  Z= 0.243
  Chirality :  0.050   0.131    528
  Planarity :  0.004   0.052    594
  Dihedral  :  4.462  12.698    462
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 12.63 %
    Favored  : 86.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.66 (0.33), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.26 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 379 
 TYR   0.007   0.001   TYR C 310 
 PHE   0.013   0.001   PHE A 378 
 HIS   0.002   0.000   HIS E 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00172 ( 3498)
  covalent geometry    : angle       0.46401 ( 4680)
  hydrogen bonds       : bond        0.01734 (   58)
  hydrogen bonds       : angle       4.08830 (  174)

*********************** 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
  33 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 30
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
REVERT: A  369 LYS cc_start: 0.8209 (tttt) cc_final: 0.7955 (ttmt)
REVERT: B  369 LYS cc_start: 0.8220 (tttt) cc_final: 0.7810 (ttmm)
REVERT: C  311 LYS cc_start: 0.7963 (pttt) cc_final: 0.7455 (pttt)
REVERT: C  345 ASP cc_start: 0.7740 (m-30) cc_final: 0.7343 (t0)
REVERT: D  311 LYS cc_start: 0.7746 (pttt) cc_final: 0.7211 (pttt)
REVERT: D  345 ASP cc_start: 0.7919 (m-30) cc_final: 0.7576 (t0)
REVERT: E  343 LYS cc_start: 0.7518 (mttt) cc_final: 0.6567 (pptt)
REVERT: E  349 ARG cc_start: 0.6334 (mtt180) cc_final: 0.4579 (pmt-80)
REVERT: F  343 LYS cc_start: 0.7345 (mttt) cc_final: 0.6437 (pptt)
REVERT: F  372 GLU cc_start: 0.7919 (tt0) cc_final: 0.7654 (mt-10)
  outliers start: 3
  outliers final: 3
  residues processed: 30
  average time/residue: 1.1796
  time to fit residues: 36.5491
Evaluate side-chains
  28 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain D residue  319 THR
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 27 optimal weight:    0.8980
   chunk 24 optimal weight:    4.9990
   chunk 6 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 34 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    0.9980
   chunk 38 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   overall best weight:    2.3384

-------------------------------------------------------------------------------
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 = 0.4863 r_free = 0.4863 target = 0.208044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4579 r_free = 0.4579 target = 0.182556 restraints weight = 12065.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.4590 rms_B_bonded: 2.08
r_work: 0.4501 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.4414 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.4414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
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      :  0.003   0.018   3498  Z= 0.119
  Angle     :  0.530   5.151   4680  Z= 0.278
  Chirality :  0.051   0.138    528
  Planarity :  0.005   0.050    594
  Dihedral  :  4.696  12.789    462
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 13.13 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -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
 ARG   0.001   0.000   ARG D 379 
 TYR   0.012   0.002   TYR C 310 
 PHE   0.013   0.002   PHE A 378 
 HIS   0.002   0.001   HIS E 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 3498)
  covalent geometry    : angle       0.52985 ( 4680)
  hydrogen bonds       : bond        0.02095 (   58)
  hydrogen bonds       : angle       4.30791 (  174)

********************** 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
  37 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
REVERT: A  369 LYS cc_start: 0.8231 (tttt) cc_final: 0.7987 (ttmt)
REVERT: B  348 ASP cc_start: 0.7827 (m-30) cc_final: 0.7621 (m-30)
REVERT: B  369 LYS cc_start: 0.8288 (tttt) cc_final: 0.7892 (ttmm)
REVERT: C  311 LYS cc_start: 0.8064 (pttt) cc_final: 0.7724 (pptt)
REVERT: C  345 ASP cc_start: 0.7784 (m-30) cc_final: 0.7391 (t0)
REVERT: D  311 LYS cc_start: 0.7791 (pttt) cc_final: 0.7255 (pttt)
REVERT: D  345 ASP cc_start: 0.8048 (m-30) cc_final: 0.7692 (t0)
REVERT: E  311 LYS cc_start: 0.8118 (ttpt) cc_final: 0.7854 (mttm)
REVERT: E  343 LYS cc_start: 0.7581 (mttt) cc_final: 0.6583 (pptt)
REVERT: E  347 LYS cc_start: 0.8376 (mttt) cc_final: 0.6346 (pptt)
REVERT: E  349 ARG cc_start: 0.6491 (mtt180) cc_final: 0.4730 (pmt-80)
REVERT: F  343 LYS cc_start: 0.7371 (mttt) cc_final: 0.6503 (pptt)
REVERT: F  372 GLU cc_start: 0.7924 (tt0) cc_final: 0.7645 (mt-10)
REVERT: F  375 LYS cc_start: 0.8113 (tttt) cc_final: 0.7688 (ttmt)
REVERT: F  378 PHE cc_start: 0.7270 (t80) cc_final: 0.7047 (t80)
  outliers start: 3
  outliers final: 3
  residues processed: 34
  average time/residue: 1.4161
  time to fit residues: 49.3942
Evaluate side-chains
  36 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain C residue  319 THR
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 39 optimal weight:    6.9990
   chunk 7 optimal weight:   10.0000
   chunk 34 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 35 optimal weight:    0.5980
   chunk 3 optimal weight:    8.9990
   chunk 8 optimal weight:    9.9990
   chunk 9 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    1.7184

-------------------------------------------------------------------------------
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 = 0.4873 r_free = 0.4873 target = 0.208891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.183742 restraints weight = 11903.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.4608 rms_B_bonded: 2.04
r_work: 0.4519 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.4433 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.4433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.4562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3498  Z= 0.095
  Angle     :  0.497   5.135   4680  Z= 0.259
  Chirality :  0.051   0.134    528
  Planarity :  0.004   0.051    594
  Dihedral  :  4.621  13.204    462
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 13.89 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.59 (0.33), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.21 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 379 
 TYR   0.009   0.002   TYR C 310 
 PHE   0.013   0.001   PHE A 378 
 HIS   0.001   0.000   HIS D 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 ( 3498)
  covalent geometry    : angle       0.49671 ( 4680)
  hydrogen bonds       : bond        0.01913 (   58)
  hydrogen bonds       : angle       4.20398 (  174)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2807.95 seconds
wall clock time: 48 minutes 14.48 seconds (2894.48 seconds total)