Starting phenix.real_space_refine
on Tue Mar 11 16:10:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q9k_18284/03_2025/8q9k_18284.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q9k_18284/03_2025/8q9k_18284.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q9k_18284/03_2025/8q9k_18284.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q9k_18284/03_2025/8q9k_18284.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q9k_18284/03_2025/8q9k_18284.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q9k_18284/03_2025/8q9k_18284.cif"
  }
  resolution = 3.2
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C    1932      2.51       5
     N     570      2.21       5
     O     582      1.98       5
     H    3216      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6306
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 1051
          Classifications: {'peptide': 68}
          Link IDs: {'PTRANS': 3, 'TRANS': 64}
    Chain: "E"
      Number of atoms: 1051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 1051
          Classifications: {'peptide': 68}
          Link IDs: {'PTRANS': 3, 'TRANS': 64}
    Chain: "C"
      Number of atoms: 1051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 1051
          Classifications: {'peptide': 68}
          Link IDs: {'PTRANS': 3, 'TRANS': 64}
    Chain: "D"
      Number of atoms: 1051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 1051
          Classifications: {'peptide': 68}
          Link IDs: {'PTRANS': 3, 'TRANS': 64}
    Chain: "B"
      Number of atoms: 1051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 1051
          Classifications: {'peptide': 68}
          Link IDs: {'PTRANS': 3, 'TRANS': 64}
    Chain: "F"
      Number of atoms: 1051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 1051
          Classifications: {'peptide': 68}
          Link IDs: {'PTRANS': 3, 'TRANS': 64}
  Time building chain proxies: 5.20, per 1000 atoms: 0.82
  Number of scatterers: 6306
  At special positions: 0
  Unit cell: (139.256, 84.048, 41.2, 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     582      8.00
     N     570      7.00
     C    1932      6.00
     H    3216      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 448.8 milliseconds
  

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  708

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 18 sheets defined
      0.0% alpha, 45.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.73
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'E' and resid 309 through 310
      removed outlier: 6.552A  pdb=" N   VAL A 309 " --> pdb=" O   TYR F 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 313 through 314
      removed outlier: 6.837A  pdb=" N   VAL A 313 " --> pdb=" O   ASP F 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 317 through 322
      removed outlier: 6.415A  pdb=" N   LYS A 317 " --> pdb=" O   VAL F 318 " (cutoff:3.500A)
      removed outlier: 8.334A  pdb=" N   SER F 320 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   THR A 319 " --> pdb=" O   SER F 320 " (cutoff:3.500A)
      removed outlier: 8.456A  pdb=" N   CYS F 322 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   LYS A 321 " --> pdb=" O   CYS F 322 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 325 through 330
      removed outlier: 6.913A  pdb=" N   GLY A 326 " --> pdb=" O   LEU E 325 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   ASN E 327 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   GLY F 326 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   ASN A 327 " --> pdb=" O   GLY F 326 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 337 through 341
      removed outlier: 6.613A  pdb=" N   VAL A 337 " --> pdb=" O   GLU E 338 " (cutoff:3.500A)
      removed outlier: 8.198A  pdb=" N   LYS E 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   VAL A 339 " --> pdb=" O   LYS E 340 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 345 through 346
      removed outlier: 6.648A  pdb=" N   ASP A 345 " --> pdb=" O   PHE F 346 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 350 through 354
      removed outlier: 6.381A  pdb=" N   VAL A 350 " --> pdb=" O   GLN E 351 " (cutoff:3.500A)
      removed outlier: 8.299A  pdb=" N   LYS E 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   SER A 352 " --> pdb=" O   LYS E 353 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 357 through 362
      removed outlier: 6.440A  pdb=" N   ASP A 358 " --> pdb=" O   ASN F 359 " (cutoff:3.500A)
      removed outlier: 8.061A  pdb=" N   THR F 361 " --> pdb=" O   ASP A 358 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ILE A 360 " --> pdb=" O   THR F 361 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 369 through 374
      removed outlier: 6.568A  pdb=" N   LYS A 369 " --> pdb=" O   LYS F 370 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   GLU F 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   ILE A 371 " --> pdb=" O   GLU F 372 " (cutoff:3.500A)
      removed outlier: 8.130A  pdb=" N   HIS F 374 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   THR A 373 " --> pdb=" O   HIS F 374 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 309 through 310
      removed outlier: 6.488A  pdb=" N   VAL C 309 " --> pdb=" O   TYR D 310 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   VAL D 309 " --> pdb=" O   TYR B 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'C' and resid 313 through 314
      removed outlier: 6.753A  pdb=" N   VAL C 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   VAL D 313 " --> pdb=" O   ASP B 314 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'C' and resid 317 through 322
      removed outlier: 6.424A  pdb=" N   LYS C 317 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
      removed outlier: 8.295A  pdb=" N   SER D 320 " --> pdb=" O   LYS C 317 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   THR C 319 " --> pdb=" O   SER D 320 " (cutoff:3.500A)
      removed outlier: 8.444A  pdb=" N   CYS D 322 " --> pdb=" O   THR C 319 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   LYS C 321 " --> pdb=" O   CYS D 322 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   LYS D 317 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 8.336A  pdb=" N   SER B 320 " --> pdb=" O   LYS D 317 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   THR D 319 " --> pdb=" O   SER B 320 " (cutoff:3.500A)
      removed outlier: 8.501A  pdb=" N   CYS B 322 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   LYS D 321 " --> pdb=" O   CYS B 322 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'C' and resid 325 through 330
      removed outlier: 8.850A  pdb=" N   LEU C 325 " --> pdb=" O   GLY D 326 " (cutoff:3.500A)
      removed outlier: 9.832A  pdb=" N   ILE D 328 " --> pdb=" O   LEU C 325 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   ASN C 327 " --> pdb=" O   ILE D 328 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   HIS D 330 " --> pdb=" O   ASN C 327 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   HIS C 329 " --> pdb=" O   HIS D 330 " (cutoff:3.500A)
      removed outlier: 8.894A  pdb=" N   LEU D 325 " --> pdb=" O   GLY B 326 " (cutoff:3.500A)
      removed outlier: 9.761A  pdb=" N   ILE B 328 " --> pdb=" O   LEU D 325 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   ASN D 327 " --> pdb=" O   ILE B 328 " (cutoff:3.500A)
      removed outlier: 7.921A  pdb=" N   HIS B 330 " --> pdb=" O   ASN D 327 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   HIS D 329 " --> pdb=" O   HIS B 330 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'C' and resid 337 through 340
    Processing sheet with id=AB6, first strand: chain 'C' and resid 345 through 346
      removed outlier: 6.564A  pdb=" N   ASP C 345 " --> pdb=" O   PHE D 346 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   ASP D 345 " --> pdb=" O   PHE B 346 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'C' and resid 350 through 354
    Processing sheet with id=AB8, first strand: chain 'C' and resid 357 through 362
      removed outlier: 6.440A  pdb=" N   ASP C 358 " --> pdb=" O   ASN D 359 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   THR D 361 " --> pdb=" O   ASP C 358 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   ILE C 360 " --> pdb=" O   THR D 361 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   ASP D 358 " --> pdb=" O   ASN B 359 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   THR B 361 " --> pdb=" O   ASP D 358 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   ILE D 360 " --> pdb=" O   THR B 361 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'C' and resid 369 through 374
      removed outlier: 6.501A  pdb=" N   LYS C 369 " --> pdb=" O   LYS D 370 " (cutoff:3.500A)
      removed outlier: 7.998A  pdb=" N   GLU D 372 " --> pdb=" O   LYS C 369 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   ILE C 371 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
      removed outlier: 8.098A  pdb=" N   HIS D 374 " --> pdb=" O   ILE C 371 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   THR C 373 " --> pdb=" O   HIS D 374 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   LYS D 369 " --> pdb=" O   LYS B 370 " (cutoff:3.500A)
      removed outlier: 8.092A  pdb=" N   GLU B 372 " --> pdb=" O   LYS D 369 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   ILE D 371 " --> pdb=" O   GLU B 372 " (cutoff:3.500A)
      removed outlier: 8.104A  pdb=" N   HIS B 374 " --> pdb=" O   ILE D 371 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   THR D 373 " --> pdb=" O   HIS B 374 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB9

    47 hydrogen bonds defined for protein.
    141 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: 2.15

  Time building geometry restraints manager: 2.00 seconds

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

  Histogram of bond lengths:
        0.95 -     1.12: 3210
        1.12 -     1.29: 522
        1.29 -     1.46: 891
        1.46 -     1.63: 1725
        1.63 -     1.81: 6
  Bond restraints: 6354
  Sorted by residual:
  bond pdb=" N   SER C 324 "
       pdb=" H   SER C 324 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" NE  ARG A 349 "
       pdb=" HE  ARG A 349 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" CD2 PHE E 346 "
       pdb=" HD2 PHE E 346 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.69e+01
  bond pdb=" N   GLU F 338 "
       pdb=" H   GLU F 338 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.68e+01
  bond pdb=" N   LYS C 311 "
       pdb=" H   LYS C 311 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.68e+01
  ... (remaining 6349 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.10: 10214
        3.10 -     6.19: 1247
        6.19 -     9.29: 133
        9.29 -    12.38: 6
       12.38 -    15.48: 4
  Bond angle restraints: 11604
  Sorted by residual:
  angle pdb=" N   GLY D 326 "
        pdb=" CA  GLY D 326 "
        pdb=" C   GLY D 326 "
      ideal   model   delta    sigma   weight residual
     110.69  117.98   -7.29 1.33e+00 5.65e-01 3.00e+01
  angle pdb=" C   LYS C 340 "
        pdb=" N   SER C 341 "
        pdb=" H   SER C 341 "
      ideal   model   delta    sigma   weight residual
     123.83  108.35   15.48 3.00e+00 1.11e-01 2.66e+01
  angle pdb=" C   LYS B 340 "
        pdb=" N   SER B 341 "
        pdb=" H   SER B 341 "
      ideal   model   delta    sigma   weight residual
     123.83  108.63   15.20 3.00e+00 1.11e-01 2.57e+01
  angle pdb=" N   ARG D 349 "
        pdb=" CA  ARG D 349 "
        pdb=" C   ARG D 349 "
      ideal   model   delta    sigma   weight residual
     110.35  117.23   -6.88 1.36e+00 5.41e-01 2.56e+01
  angle pdb=" C   LYS D 340 "
        pdb=" N   SER D 341 "
        pdb=" H   SER D 341 "
      ideal   model   delta    sigma   weight residual
     123.83  108.95   14.88 3.00e+00 1.11e-01 2.46e+01
  ... (remaining 11599 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.63: 2579
       13.63 -    27.26: 156
       27.26 -    40.89: 58
       40.89 -    54.52: 42
       54.52 -    68.15: 87
  Dihedral angle restraints: 2922
    sinusoidal: 1680
      harmonic: 1242
  Sorted by residual:
  dihedral pdb=" C   ARG B 349 "
           pdb=" N   ARG B 349 "
           pdb=" CA  ARG B 349 "
           pdb=" CB  ARG B 349 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.04   10.44     0      2.50e+00 1.60e-01 1.75e+01
  dihedral pdb=" C   ARG F 349 "
           pdb=" N   ARG F 349 "
           pdb=" CA  ARG F 349 "
           pdb=" CB  ARG F 349 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.63   10.03     0      2.50e+00 1.60e-01 1.61e+01
  dihedral pdb=" N   ARG B 349 "
           pdb=" C   ARG B 349 "
           pdb=" CA  ARG B 349 "
           pdb=" CB  ARG B 349 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  131.83   -9.03     0      2.50e+00 1.60e-01 1.31e+01
  ... (remaining 2919 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.085: 323
       0.085 -    0.169: 124
       0.169 -    0.254: 16
       0.254 -    0.338: 2
       0.338 -    0.423: 3
  Chirality restraints: 468
  Sorted by residual:
  chirality pdb=" CA  ARG B 349 "
            pdb=" N   ARG B 349 "
            pdb=" C   ARG B 349 "
            pdb=" CB  ARG B 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.47e+00
  chirality pdb=" CA  ARG F 349 "
            pdb=" N   ARG F 349 "
            pdb=" C   ARG F 349 "
            pdb=" CB  ARG F 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.02e+00
  chirality pdb=" CA  ARG D 349 "
            pdb=" N   ARG D 349 "
            pdb=" C   ARG D 349 "
            pdb=" CB  ARG D 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.38 2.00e-01 2.50e+01 3.52e+00
  ... (remaining 465 not shown)

  Planarity restraints: 918
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 340 "    0.046 2.00e-02 2.50e+03   8.41e-02 7.07e+01
        pdb=" N   SER B 341 "   -0.145 2.00e-02 2.50e+03
        pdb=" CA  SER B 341 "    0.045 2.00e-02 2.50e+03
        pdb=" H   SER B 341 "    0.055 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 340 "    0.044 2.00e-02 2.50e+03   7.88e-02 6.21e+01
        pdb=" N   SER C 341 "   -0.136 2.00e-02 2.50e+03
        pdb=" CA  SER C 341 "    0.042 2.00e-02 2.50e+03
        pdb=" H   SER C 341 "    0.051 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS D 340 "    0.041 2.00e-02 2.50e+03   7.42e-02 5.51e+01
        pdb=" N   SER D 341 "   -0.128 2.00e-02 2.50e+03
        pdb=" CA  SER D 341 "    0.039 2.00e-02 2.50e+03
        pdb=" H   SER D 341 "    0.048 2.00e-02 2.50e+03
  ... (remaining 915 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 475
        2.18 -     2.78: 10985
        2.78 -     3.39: 16438
        3.39 -     3.99: 21542
        3.99 -     4.60: 30268
  Nonbonded interactions: 79708
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP E 314 "
            pdb=" HG  SER E 316 "
     model   vdw
     1.571 2.450
  nonbonded pdb=" OD1 ASP C 314 "
            pdb=" HG  SER C 316 "
     model   vdw
     1.573 2.450
  nonbonded pdb=" OD1 ASP D 314 "
            pdb=" HG  SER D 316 "
     model   vdw
     1.579 2.450
  nonbonded pdb=" OD1 ASP A 314 "
            pdb=" HG  SER A 316 "
     model   vdw
     1.583 2.450
  nonbonded pdb=" OD1 ASP F 314 "
            pdb=" HG  SER F 316 "
     model   vdw
     1.597 2.450
  ... (remaining 79703 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:             2.260
  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:             0.110
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.380
  Find NCS groups from input model:        0.160
  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:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
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      :  0.011   0.038   3138  Z= 0.741
  Angle     :  1.997   7.291   4194  Z= 1.327
  Chirality :  0.088   0.423    468
  Planarity :  0.011   0.092    534
  Dihedral  :  9.094  65.306   1212
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 0.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.94 (0.34), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.47 (0.26), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.016   0.003   HIS B 330 
 PHE   0.037   0.018   PHE D 346 
 TYR   0.049   0.014   TYR D 310 
 ARG   0.007   0.001   ARG F 349 

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  317 LYS cc_start: 0.8756 (pttt) cc_final: 0.7914 (mmmt)
REVERT: C  317 LYS cc_start: 0.8615 (pttt) cc_final: 0.7747 (mmtt)
REVERT: C  345 ASP cc_start: 0.7730 (t0) cc_final: 0.7432 (t70)
REVERT: F  340 LYS cc_start: 0.7983 (ttmt) cc_final: 0.7594 (tttm)
  outliers start: 0
  outliers final: 0
  residues processed: 151
  average time/residue: 0.5827
  time to fit residues: 97.1958
Evaluate side-chains
  90 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 14 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   overall best weight:    1.1786

-------------------------------------------------------------------------------
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 = 0.4443 r_free = 0.4443 target = 0.169618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.133681 restraints weight = 10669.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.4197 rms_B_bonded: 2.40
r_work: 0.4104 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.4004 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.4004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.5172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3138  Z= 0.173
  Angle     :  0.549   4.332   4194  Z= 0.287
  Chirality :  0.052   0.135    468
  Planarity :  0.004   0.032    534
  Dihedral  :  5.534  19.091    414
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 1.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  7.63 %
    Favored  : 91.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.34), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.35 (0.26), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D 330 
 PHE   0.006   0.002   PHE D 346 
 TYR   0.003   0.001   TYR E 310 
 ARG   0.001   0.000   ARG D 349 

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.513 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 THR cc_start: 0.8669 (m) cc_final: 0.8439 (p)
REVERT: E  317 LYS cc_start: 0.8818 (pttt) cc_final: 0.7034 (mmmt)
REVERT: E  340 LYS cc_start: 0.8295 (ttmt) cc_final: 0.8040 (tttt)
REVERT: E  372 GLU cc_start: 0.5916 (pm20) cc_final: 0.5675 (pm20)
REVERT: C  317 LYS cc_start: 0.8766 (pttt) cc_final: 0.6963 (mmmt)
REVERT: C  345 ASP cc_start: 0.8348 (t0) cc_final: 0.8007 (t0)
REVERT: C  347 LYS cc_start: 0.8647 (mmtt) cc_final: 0.8245 (mmtm)
REVERT: D  331 LYS cc_start: 0.8269 (mtpt) cc_final: 0.7456 (tptt)
REVERT: D  345 ASP cc_start: 0.8335 (t70) cc_final: 0.7570 (t0)
REVERT: D  347 LYS cc_start: 0.8762 (mmtp) cc_final: 0.8188 (mmtt)
REVERT: D  372 GLU cc_start: 0.8269 (tt0) cc_final: 0.7748 (tp30)
REVERT: B  345 ASP cc_start: 0.8241 (t70) cc_final: 0.7965 (t0)
REVERT: F  369 LYS cc_start: 0.8851 (mtmt) cc_final: 0.8372 (mtmm)
  outliers start: 4
  outliers final: 4
  residues processed: 106
  average time/residue: 0.4731
  time to fit residues: 56.9409
Evaluate side-chains
  96 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 92
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  313 VAL
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain F residue  309 VAL
Chi-restraints excluded: chain F residue  356 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 8 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 21 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 1 optimal weight:    6.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.162674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.126569 restraints weight = 11056.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.4102 rms_B_bonded: 2.36
r_work: 0.4013 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3917 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.5643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3138  Z= 0.291
  Angle     :  0.552   4.123   4194  Z= 0.290
  Chirality :  0.052   0.132    468
  Planarity :  0.004   0.036    534
  Dihedral  :  5.403  18.691    414
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 1.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  :  7.91 %
    Favored  : 89.83 %
  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: -1.80 (0.34), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.36 (0.26), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS F 330 
 PHE   0.007   0.002   PHE E 346 
 TYR   0.005   0.001   TYR E 310 
 ARG   0.001   0.000   ARG D 349 

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.580 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 THR cc_start: 0.8729 (m) cc_final: 0.8505 (p)
REVERT: A  373 THR cc_start: 0.8895 (m) cc_final: 0.8430 (p)
REVERT: E  317 LYS cc_start: 0.8870 (pttt) cc_final: 0.7084 (mmmt)
REVERT: E  369 LYS cc_start: 0.8854 (mtpt) cc_final: 0.8406 (mtmt)
REVERT: C  317 LYS cc_start: 0.8838 (pttt) cc_final: 0.7055 (mmmt)
REVERT: C  345 ASP cc_start: 0.8323 (t0) cc_final: 0.7941 (t0)
REVERT: C  347 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8323 (mmtm)
REVERT: D  345 ASP cc_start: 0.8368 (t70) cc_final: 0.7710 (t0)
REVERT: D  347 LYS cc_start: 0.8785 (mmtp) cc_final: 0.8225 (mmtt)
REVERT: D  372 GLU cc_start: 0.8336 (tt0) cc_final: 0.7822 (tp30)
REVERT: B  345 ASP cc_start: 0.8343 (t70) cc_final: 0.8124 (t0)
  outliers start: 8
  outliers final: 8
  residues processed: 93
  average time/residue: 0.5022
  time to fit residues: 52.8361
Evaluate side-chains
  89 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain E residue  309 VAL
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain C residue  309 VAL
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain F residue  309 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 12 optimal weight:   10.0000
   chunk 6 optimal weight:    8.9990
   chunk 25 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    1.5788

-------------------------------------------------------------------------------
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 = 0.4419 r_free = 0.4419 target = 0.167109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.131045 restraints weight = 10958.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.4158 rms_B_bonded: 2.40
r_work: 0.4056 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3960 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.5840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3138  Z= 0.189
  Angle     :  0.497   4.304   4194  Z= 0.258
  Chirality :  0.052   0.134    468
  Planarity :  0.004   0.037    534
  Dihedral  :  5.072  17.622    414
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  :  9.89 %
    Favored  : 88.42 %
  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: -1.81 (0.33), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.37 (0.26), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 330 
 PHE   0.003   0.001   PHE A 346 
 TYR   0.004   0.001   TYR E 310 
 ARG   0.001   0.000   ARG E 349 

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 THR cc_start: 0.8615 (m) cc_final: 0.8407 (p)
REVERT: A  372 GLU cc_start: 0.8361 (tt0) cc_final: 0.7928 (tp30)
REVERT: E  317 LYS cc_start: 0.8772 (pttt) cc_final: 0.7001 (mmmt)
REVERT: E  340 LYS cc_start: 0.8226 (ttmt) cc_final: 0.7977 (tttt)
REVERT: E  348 ASP cc_start: 0.8640 (t0) cc_final: 0.8434 (t0)
REVERT: E  349 ARG cc_start: 0.7828 (ptp-170) cc_final: 0.5046 (mmm-85)
REVERT: C  317 LYS cc_start: 0.8778 (pttt) cc_final: 0.6999 (mmmt)
REVERT: C  345 ASP cc_start: 0.8299 (t0) cc_final: 0.7881 (t0)
REVERT: C  347 LYS cc_start: 0.8728 (mmtt) cc_final: 0.8267 (mmtm)
REVERT: C  349 ARG cc_start: 0.7964 (ptp-170) cc_final: 0.5064 (mmm-85)
REVERT: D  345 ASP cc_start: 0.8348 (t70) cc_final: 0.7642 (t0)
REVERT: D  347 LYS cc_start: 0.8753 (mmtp) cc_final: 0.8173 (mmtt)
REVERT: D  372 GLU cc_start: 0.8330 (tt0) cc_final: 0.7787 (tp30)
REVERT: B  345 ASP cc_start: 0.8328 (t70) cc_final: 0.8072 (t0)
  outliers start: 6
  outliers final: 6
  residues processed: 92
  average time/residue: 0.5126
  time to fit residues: 53.0348
Evaluate side-chains
  94 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain F residue  309 VAL
Chi-restraints excluded: chain F residue  356 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 14 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   chunk 1 optimal weight:    9.9990
   chunk 9 optimal weight:    4.9990
   chunk 2 optimal weight:    0.7980
   chunk 23 optimal weight:    0.3980
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 = 0.4442 r_free = 0.4442 target = 0.169069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.133070 restraints weight = 10781.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.4183 rms_B_bonded: 2.42
r_work: 0.4085 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3989 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.5993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   3138  Z= 0.171
  Angle     :  0.474   4.049   4194  Z= 0.244
  Chirality :  0.051   0.133    468
  Planarity :  0.004   0.038    534
  Dihedral  :  4.759  16.937    414
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  :  9.89 %
    Favored  : 88.14 %
  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 (0.34), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.28 (0.26), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 330 
 PHE   0.003   0.001   PHE E 346 
 TYR   0.004   0.001   TYR E 310 
 ARG   0.001   0.000   ARG A 349 

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 THR cc_start: 0.8616 (m) cc_final: 0.8388 (p)
REVERT: A  372 GLU cc_start: 0.8314 (tt0) cc_final: 0.7917 (tp30)
REVERT: E  317 LYS cc_start: 0.8768 (pttt) cc_final: 0.6977 (mmmt)
REVERT: E  340 LYS cc_start: 0.8263 (ttmt) cc_final: 0.8017 (tttt)
REVERT: E  349 ARG cc_start: 0.7850 (ptp-170) cc_final: 0.5018 (mmm-85)
REVERT: C  317 LYS cc_start: 0.8753 (pttt) cc_final: 0.6952 (mmmt)
REVERT: C  345 ASP cc_start: 0.8272 (t0) cc_final: 0.7873 (t0)
REVERT: C  347 LYS cc_start: 0.8724 (mmtt) cc_final: 0.8316 (mmtm)
REVERT: C  349 ARG cc_start: 0.7925 (ptp-170) cc_final: 0.5068 (mmm-85)
REVERT: D  345 ASP cc_start: 0.8286 (t70) cc_final: 0.7604 (t0)
REVERT: D  347 LYS cc_start: 0.8725 (mmtp) cc_final: 0.8094 (mmtt)
REVERT: D  349 ARG cc_start: 0.7573 (ptp90) cc_final: 0.7210 (ptm160)
REVERT: D  372 GLU cc_start: 0.8333 (tt0) cc_final: 0.7802 (tp30)
REVERT: B  345 ASP cc_start: 0.8298 (t70) cc_final: 0.8022 (t0)
REVERT: F  345 ASP cc_start: 0.8249 (t0) cc_final: 0.7758 (t0)
REVERT: F  347 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8542 (mmtt)
  outliers start: 7
  outliers final: 7
  residues processed: 95
  average time/residue: 0.5125
  time to fit residues: 54.8652
Evaluate side-chains
  95 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  309 VAL
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain F residue  309 VAL
Chi-restraints excluded: chain F residue  356 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 31 optimal weight:    7.9990
   chunk 18 optimal weight:   10.0000
   chunk 11 optimal weight:    3.9990
   chunk 7 optimal weight:    8.9990
   chunk 32 optimal weight:    0.8980
   chunk 13 optimal weight:    9.9990
   chunk 28 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.164465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.128183 restraints weight = 10800.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.4127 rms_B_bonded: 2.37
r_work: 0.4027 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3932 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.6071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3138  Z= 0.246
  Angle     :  0.501   4.457   4194  Z= 0.262
  Chirality :  0.051   0.131    468
  Planarity :  0.004   0.040    534
  Dihedral  :  4.973  16.313    414
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 11.30 %
    Favored  : 86.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.34), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.35 (0.26), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 329 
 PHE   0.005   0.001   PHE D 346 
 TYR   0.004   0.001   TYR E 310 
 ARG   0.000   0.000   ARG D 349 

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.655 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 THR cc_start: 0.8645 (m) cc_final: 0.8427 (p)
REVERT: E  317 LYS cc_start: 0.8803 (pttt) cc_final: 0.6998 (mmmt)
REVERT: E  349 ARG cc_start: 0.7983 (ptp-170) cc_final: 0.5059 (mmm-85)
REVERT: C  317 LYS cc_start: 0.8804 (pttt) cc_final: 0.7014 (mmmt)
REVERT: C  345 ASP cc_start: 0.8265 (t0) cc_final: 0.7847 (t0)
REVERT: C  347 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8342 (mmtm)
REVERT: C  349 ARG cc_start: 0.8019 (ptp-170) cc_final: 0.5298 (mmm-85)
REVERT: D  345 ASP cc_start: 0.8264 (t70) cc_final: 0.7576 (t0)
REVERT: D  347 LYS cc_start: 0.8767 (mmtp) cc_final: 0.8166 (mmtt)
REVERT: D  349 ARG cc_start: 0.7634 (ptp90) cc_final: 0.7193 (ptm160)
REVERT: D  372 GLU cc_start: 0.8300 (tt0) cc_final: 0.7805 (tp30)
REVERT: B  345 ASP cc_start: 0.8337 (t70) cc_final: 0.8084 (t0)
REVERT: F  345 ASP cc_start: 0.8389 (t0) cc_final: 0.8006 (t0)
REVERT: F  347 LYS cc_start: 0.8827 (mmtt) cc_final: 0.8574 (mmtt)
  outliers start: 8
  outliers final: 8
  residues processed: 90
  average time/residue: 0.5472
  time to fit residues: 55.6143
Evaluate side-chains
  92 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  309 VAL
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain C residue  309 VAL
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain F residue  309 VAL
Chi-restraints excluded: chain F residue  356 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 7 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 12 optimal weight:    6.9990
   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 = 0.4415 r_free = 0.4415 target = 0.165955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.129978 restraints weight = 10956.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.4152 rms_B_bonded: 2.42
r_work: 0.4051 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3955 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.6178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3138  Z= 0.198
  Angle     :  0.478   4.158   4194  Z= 0.247
  Chirality :  0.051   0.132    468
  Planarity :  0.004   0.040    534
  Dihedral  :  4.821  16.445    414
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 11.30 %
    Favored  : 86.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.34), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.30 (0.26), residues: 396

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

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 0.582 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 THR cc_start: 0.8632 (m) cc_final: 0.8408 (p)
REVERT: A  372 GLU cc_start: 0.8365 (tt0) cc_final: 0.7884 (tp30)
REVERT: E  317 LYS cc_start: 0.8771 (pttt) cc_final: 0.6977 (mmmt)
REVERT: E  340 LYS cc_start: 0.8248 (ttmt) cc_final: 0.8039 (tttt)
REVERT: E  349 ARG cc_start: 0.7911 (ptp-170) cc_final: 0.5239 (mmm160)
REVERT: C  317 LYS cc_start: 0.8791 (pttt) cc_final: 0.7048 (mmmt)
REVERT: C  345 ASP cc_start: 0.8227 (t0) cc_final: 0.7796 (t0)
REVERT: C  347 LYS cc_start: 0.8720 (mmtt) cc_final: 0.8290 (mmtm)
REVERT: C  349 ARG cc_start: 0.8005 (ptp-170) cc_final: 0.5377 (mmm160)
REVERT: D  345 ASP cc_start: 0.8291 (t70) cc_final: 0.7585 (t0)
REVERT: D  347 LYS cc_start: 0.8759 (mmtp) cc_final: 0.8147 (mmtt)
REVERT: D  349 ARG cc_start: 0.7618 (ptp90) cc_final: 0.7195 (ptm160)
REVERT: D  372 GLU cc_start: 0.8299 (tt0) cc_final: 0.7822 (tp30)
REVERT: B  345 ASP cc_start: 0.8363 (t70) cc_final: 0.8107 (t0)
REVERT: F  345 ASP cc_start: 0.8256 (t0) cc_final: 0.8012 (t0)
REVERT: F  347 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8563 (mmtt)
  outliers start: 7
  outliers final: 7
  residues processed: 92
  average time/residue: 0.5444
  time to fit residues: 56.1756
Evaluate side-chains
  94 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  309 VAL
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain C residue  309 VAL
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain F residue  356 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 8 optimal weight:    4.9990
   chunk 18 optimal weight:    9.9990
   chunk 13 optimal weight:    9.9990
   chunk 29 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 26 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.8988

-------------------------------------------------------------------------------
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 = 0.4416 r_free = 0.4416 target = 0.166239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.129995 restraints weight = 10889.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.4147 rms_B_bonded: 2.40
r_work: 0.4046 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3949 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.6259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3138  Z= 0.213
  Angle     :  0.485   4.473   4194  Z= 0.251
  Chirality :  0.051   0.130    468
  Planarity :  0.004   0.037    534
  Dihedral  :  4.806  15.918    414
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 11.30 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.34), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.27 (0.26), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 329 
 PHE   0.003   0.001   PHE D 346 
 TYR   0.004   0.001   TYR E 310 
 ARG   0.000   0.000   ARG F 349 

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  317 LYS cc_start: 0.8772 (pttt) cc_final: 0.6994 (mmmt)
REVERT: E  349 ARG cc_start: 0.7936 (ptp-170) cc_final: 0.5255 (mmm160)
REVERT: C  317 LYS cc_start: 0.8783 (pttt) cc_final: 0.7043 (mmmt)
REVERT: C  345 ASP cc_start: 0.8210 (t0) cc_final: 0.7788 (t0)
REVERT: C  347 LYS cc_start: 0.8712 (mmtt) cc_final: 0.8289 (mmtm)
REVERT: C  349 ARG cc_start: 0.8044 (ptp-170) cc_final: 0.5442 (mmm160)
REVERT: D  345 ASP cc_start: 0.8267 (t70) cc_final: 0.7553 (t0)
REVERT: D  347 LYS cc_start: 0.8767 (mmtp) cc_final: 0.8139 (mmtt)
REVERT: D  372 GLU cc_start: 0.8283 (tt0) cc_final: 0.7752 (tp30)
REVERT: B  314 ASP cc_start: 0.8559 (t0) cc_final: 0.8302 (t0)
REVERT: B  345 ASP cc_start: 0.8354 (t70) cc_final: 0.8094 (t0)
REVERT: B  372 GLU cc_start: 0.7936 (mm-30) cc_final: 0.6726 (mm-30)
REVERT: F  345 ASP cc_start: 0.8245 (t0) cc_final: 0.7998 (t0)
REVERT: F  347 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8562 (mmtt)
REVERT: F  358 ASP cc_start: 0.8433 (t0) cc_final: 0.8212 (t0)
  outliers start: 9
  outliers final: 8
  residues processed: 94
  average time/residue: 0.5794
  time to fit residues: 61.8591
Evaluate side-chains
  94 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain E residue  309 VAL
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain C residue  309 VAL
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain F residue  356 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   chunk 25 optimal weight:    9.9990
   chunk 31 optimal weight:    6.9990
   chunk 9 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.4464 r_free = 0.4464 target = 0.170032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.133678 restraints weight = 10821.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.4197 rms_B_bonded: 2.44
r_work: 0.4097 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3998 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.6395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3138  Z= 0.154
  Angle     :  0.470   4.790   4194  Z= 0.238
  Chirality :  0.051   0.133    468
  Planarity :  0.004   0.037    534
  Dihedral  :  4.496  15.813    414
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 11.02 %
    Favored  : 87.01 %
  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: -1.56 (0.34), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.18 (0.26), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS F 330 
 PHE   0.002   0.001   PHE C 346 
 TYR   0.004   0.001   TYR A 310 
 ARG   0.003   0.001   ARG C 349 

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  317 LYS cc_start: 0.8768 (pttt) cc_final: 0.6961 (mmmt)
REVERT: E  349 ARG cc_start: 0.7884 (ptp-170) cc_final: 0.5100 (mmp80)
REVERT: C  317 LYS cc_start: 0.8772 (pttt) cc_final: 0.7008 (mmmt)
REVERT: C  345 ASP cc_start: 0.8235 (t0) cc_final: 0.7819 (t0)
REVERT: C  347 LYS cc_start: 0.8742 (mmtt) cc_final: 0.8302 (mmtm)
REVERT: C  349 ARG cc_start: 0.7960 (ptp-170) cc_final: 0.5015 (mmm160)
REVERT: D  345 ASP cc_start: 0.8277 (t70) cc_final: 0.7642 (t0)
REVERT: D  347 LYS cc_start: 0.8784 (mmtp) cc_final: 0.8176 (mmtt)
REVERT: B  314 ASP cc_start: 0.8605 (t0) cc_final: 0.8372 (t0)
REVERT: B  345 ASP cc_start: 0.8350 (t70) cc_final: 0.8081 (t0)
REVERT: B  372 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7694 (tt0)
  outliers start: 7
  outliers final: 7
  residues processed: 99
  average time/residue: 0.5162
  time to fit residues: 57.3556
Evaluate side-chains
  97 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain C residue  309 VAL
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain F residue  356 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 13 optimal weight:    8.9990
   chunk 10 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 7 optimal weight:    9.9990
   chunk 25 optimal weight:    0.1980
   chunk 3 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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 = 0.4471 r_free = 0.4471 target = 0.169677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.133078 restraints weight = 10853.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.4202 rms_B_bonded: 2.45
r_work: 0.4099 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3997 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.6438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3138  Z= 0.181
  Angle     :  0.479   4.571   4194  Z= 0.245
  Chirality :  0.051   0.132    468
  Planarity :  0.004   0.037    534
  Dihedral  :  4.490  15.176    414
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 11.86 %
    Favored  : 86.16 %
  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: -1.57 (0.34), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.19 (0.26), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F 330 
 PHE   0.002   0.001   PHE A 346 
 TYR   0.004   0.001   TYR E 310 
 ARG   0.002   0.000   ARG D 349 

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  372 GLU cc_start: 0.7628 (tp30) cc_final: 0.7378 (tp30)
REVERT: E  317 LYS cc_start: 0.8758 (pttt) cc_final: 0.6989 (mmmt)
REVERT: E  349 ARG cc_start: 0.7905 (ptp-170) cc_final: 0.5287 (mmm160)
REVERT: C  317 LYS cc_start: 0.8769 (pttt) cc_final: 0.7009 (mmmt)
REVERT: C  345 ASP cc_start: 0.8235 (t0) cc_final: 0.8017 (t0)
REVERT: C  349 ARG cc_start: 0.8049 (ptp-170) cc_final: 0.5101 (mmm160)
REVERT: D  345 ASP cc_start: 0.8241 (t70) cc_final: 0.7564 (t0)
REVERT: D  347 LYS cc_start: 0.8752 (mmtp) cc_final: 0.8147 (mmtt)
REVERT: B  314 ASP cc_start: 0.8618 (t0) cc_final: 0.8362 (t0)
REVERT: B  345 ASP cc_start: 0.8364 (t70) cc_final: 0.8107 (t0)
REVERT: B  372 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7678 (tt0)
REVERT: F  345 ASP cc_start: 0.8256 (t0) cc_final: 0.8046 (t0)
REVERT: F  347 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8584 (mmtt)
REVERT: F  358 ASP cc_start: 0.8448 (t0) cc_final: 0.8223 (t0)
REVERT: F  372 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7437 (tt0)
  outliers start: 7
  outliers final: 7
  residues processed: 93
  average time/residue: 0.5008
  time to fit residues: 52.7875
Evaluate side-chains
  96 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain C residue  309 VAL
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain F residue  356 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 19 optimal weight:    9.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.164076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.127356 restraints weight = 11120.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.4125 rms_B_bonded: 2.43
r_work: 0.4020 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3918 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.6454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3138  Z= 0.304
  Angle     :  0.524   4.462   4194  Z= 0.271
  Chirality :  0.051   0.130    468
  Planarity :  0.004   0.036    534
  Dihedral  :  4.983  15.516    414
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 12.43 %
    Favored  : 85.59 %
  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: -1.73 (0.34), residues: 396
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.31 (0.26), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS A 329 
 PHE   0.005   0.002   PHE E 346 
 TYR   0.004   0.001   TYR E 310 
 ARG   0.003   0.001   ARG D 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4680.21 seconds
wall clock time: 80 minutes 8.22 seconds (4808.22 seconds total)