Starting phenix.real_space_refine
on Wed Mar 12 02:33:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q9d_18277/03_2025/8q9d_18277.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q9d_18277/03_2025/8q9d_18277.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q9d_18277/03_2025/8q9d_18277.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q9d_18277/03_2025/8q9d_18277.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q9d_18277/03_2025/8q9d_18277.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q9d_18277/03_2025/8q9d_18277.cif"
  }
  resolution = 3.16
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 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 12 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7032
  Number of models: 1
  Model: ""
    Number of chains: 6
    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: "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: "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}
    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}
  Time building chain proxies: 4.28, per 1000 atoms: 0.61
  Number of scatterers: 7032
  At special positions: 0
  Unit cell: (113.712, 124.424, 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     642      8.00
     N     636      7.00
     C    2160      6.00
     H    3588      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.75
  Conformation dependent library (CDL) restraints added in 603.1 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 20 sheets defined
      0.0% alpha, 49.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'E' and resid 306 through 310
      removed outlier: 6.512A  pdb=" N   VAL E 306 " --> pdb=" O   GLN F 307 " (cutoff:3.500A)
      removed outlier: 7.976A  pdb=" N   VAL F 309 " --> pdb=" O   VAL E 306 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   ILE E 308 " --> pdb=" O   VAL F 309 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 313 through 314
      removed outlier: 6.749A  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 320
      removed outlier: 6.295A  pdb=" N   LYS A 317 " --> pdb=" O   VAL F 318 " (cutoff:3.500A)
      removed outlier: 8.434A  pdb=" N   SER F 320 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   THR A 319 " --> pdb=" O   SER F 320 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 323 through 325
      removed outlier: 6.680A  pdb=" N   SER E 324 " --> pdb=" O   LEU F 325 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 328 through 330
      removed outlier: 6.605A  pdb=" N   HIS E 329 " --> pdb=" O   HIS F 330 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 337 through 342
      removed outlier: 6.468A  pdb=" N   GLU A 338 " --> pdb=" O   VAL F 339 " (cutoff:3.500A)
      removed outlier: 7.919A  pdb=" N   SER F 341 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   LYS A 340 " --> pdb=" O   SER F 341 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 345 through 346
      removed outlier: 6.604A  pdb=" N   ASP A 345 " --> pdb=" O   PHE F 346 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 350 through 362
      removed outlier: 6.943A  pdb=" N   GLN E 351 " --> pdb=" O   VAL F 350 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   SER F 352 " --> pdb=" O   GLN E 351 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   LYS E 353 " --> pdb=" O   SER F 352 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   ILE F 354 " --> pdb=" O   LYS E 353 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   GLY E 355 " --> pdb=" O   ILE F 354 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   SER F 356 " --> pdb=" O   GLY E 355 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   GLN F 351 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   SER A 352 " --> pdb=" O   GLN F 351 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   LYS F 353 " --> pdb=" O   SER A 352 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   ILE A 354 " --> pdb=" O   LYS F 353 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   GLY F 355 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   SER A 356 " --> pdb=" O   GLY F 355 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 368 through 374
      removed outlier: 6.693A  pdb=" N   ASN E 368 " --> pdb=" O   LYS F 369 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   ILE F 371 " --> pdb=" O   ASN E 368 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   LYS E 370 " --> pdb=" O   ILE F 371 " (cutoff:3.500A)
      removed outlier: 8.122A  pdb=" N   THR F 373 " --> pdb=" O   LYS E 370 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   GLU E 372 " --> pdb=" O   THR F 373 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   LYS A 369 " --> pdb=" O   LYS F 370 " (cutoff:3.500A)
      removed outlier: 7.934A  pdb=" N   GLU F 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   ILE A 371 " --> pdb=" O   GLU F 372 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   HIS F 374 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 6.225A  pdb=" N   THR A 373 " --> pdb=" O   HIS F 374 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'E' and resid 377 through 378
      removed outlier: 6.776A  pdb=" N   THR A 377 " --> pdb=" O   PHE F 378 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 306 through 310
      removed outlier: 6.598A  pdb=" N   VAL B 306 " --> pdb=" O   GLN D 307 " (cutoff:3.500A)
      removed outlier: 8.027A  pdb=" N   VAL D 309 " --> pdb=" O   VAL B 306 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   ILE B 308 " --> pdb=" O   VAL D 309 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   GLN C 307 " --> pdb=" O   ILE D 308 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   TYR D 310 " --> pdb=" O   GLN C 307 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   VAL C 309 " --> pdb=" O   TYR D 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 313 through 314
      removed outlier: 6.759A  pdb=" N   VAL C 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 317 through 320
      removed outlier: 6.387A  pdb=" N   LYS C 317 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
      removed outlier: 8.470A  pdb=" N   SER D 320 " --> pdb=" O   LYS C 317 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   THR C 319 " --> pdb=" O   SER D 320 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 323 through 325
      removed outlier: 6.633A  pdb=" N   SER B 324 " --> pdb=" O   LEU D 325 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 328 through 330
      removed outlier: 6.549A  pdb=" N   HIS B 329 " --> pdb=" O   HIS D 330 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   ILE C 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'B' and resid 337 through 342
    Processing sheet with id=AB8, first strand: chain 'B' and resid 345 through 346
      removed outlier: 6.707A  pdb=" N   ASP C 345 " --> pdb=" O   PHE D 346 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 350 through 362
      removed outlier: 6.228A  pdb=" N   VAL B 350 " --> pdb=" O   GLN D 351 " (cutoff:3.500A)
      removed outlier: 7.872A  pdb=" N   LYS D 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   SER B 352 " --> pdb=" O   LYS D 353 " (cutoff:3.500A)
      removed outlier: 8.287A  pdb=" N   GLY D 355 " --> pdb=" O   SER B 352 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   ILE B 354 " --> pdb=" O   GLY D 355 " (cutoff:3.500A)
      removed outlier: 7.238A  pdb=" N   LEU D 357 " --> pdb=" O   ILE B 354 " (cutoff:3.500A)
      removed outlier: 7.617A  pdb=" N   SER B 356 " --> pdb=" O   LEU D 357 " (cutoff:3.500A)
      removed outlier: 10.375A  pdb=" N   ASN D 359 " --> pdb=" O   SER B 356 " (cutoff:3.500A)
      removed outlier: 9.096A  pdb=" N   ASP B 358 " --> pdb=" O   ASN D 359 " (cutoff:3.500A)
      removed outlier: 10.089A  pdb=" N   THR D 361 " --> pdb=" O   ASP B 358 " (cutoff:3.500A)
      removed outlier: 9.063A  pdb=" N   ILE B 360 " --> pdb=" O   THR D 361 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   LEU C 357 " --> pdb=" O   SER D 356 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   ASP D 358 " --> pdb=" O   LEU C 357 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   ASN C 359 " --> pdb=" O   ASP D 358 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   ILE D 360 " --> pdb=" O   ASN C 359 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   THR C 361 " --> pdb=" O   ILE D 360 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   HIS D 362 " --> pdb=" O   THR C 361 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 368 through 374
      removed outlier: 6.442A  pdb=" N   LYS C 369 " --> pdb=" O   LYS D 370 " (cutoff:3.500A)
      removed outlier: 7.779A  pdb=" N   GLU D 372 " --> pdb=" O   LYS C 369 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   ILE C 371 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
      removed outlier: 8.211A  pdb=" N   HIS D 374 " --> pdb=" O   ILE C 371 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   THR C 373 " --> pdb=" O   HIS D 374 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 377 through 378
      removed outlier: 6.837A  pdb=" N   THR C 377 " --> pdb=" O   PHE D 378 " (cutoff:3.500A)

    61 hydrogen bonds defined for protein.
    183 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: 2.10

  Time building geometry restraints manager: 2.15 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: 3582
        1.12 -     1.29: 570
        1.29 -     1.47: 1156
        1.47 -     1.64: 1772
        1.64 -     1.81: 6
  Bond restraints: 7086
  Sorted by residual:
  bond pdb=" N   SER B 316 "
       pdb=" H   SER B 316 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" N   LYS D 311 "
       pdb=" H   LYS D 311 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.65e+01
  bond pdb=" CE1 PHE C 346 "
       pdb=" HE1 PHE C 346 "
    ideal  model  delta    sigma   weight residual
    0.930  1.080 -0.150 2.00e-02 2.50e+03 5.65e+01
  bond pdb=" N   PHE E 378 "
       pdb=" H   PHE E 378 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.65e+01
  bond pdb=" N   VAL A 309 "
       pdb=" H   VAL A 309 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.64e+01
  ... (remaining 7081 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.58: 11102
        2.58 -     5.16: 1380
        5.16 -     7.74: 409
        7.74 -    10.33: 15
       10.33 -    12.91: 6
  Bond angle restraints: 12912
  Sorted by residual:
  angle pdb=" CB  HIS D 330 "
        pdb=" CG  HIS D 330 "
        pdb=" CD2 HIS D 330 "
      ideal   model   delta    sigma   weight residual
     131.20  124.69    6.51 1.30e+00 5.92e-01 2.51e+01
  angle pdb=" C   ASP A 348 "
        pdb=" N   ARG A 349 "
        pdb=" CA  ARG A 349 "
      ideal   model   delta    sigma   weight residual
     121.05  127.97   -6.92 1.43e+00 4.89e-01 2.35e+01
  angle pdb=" CA  ASP B 348 "
        pdb=" CB  ASP B 348 "
        pdb=" CG  ASP B 348 "
      ideal   model   delta    sigma   weight residual
     112.60  117.28   -4.68 1.00e+00 1.00e+00 2.19e+01
  angle pdb=" CB  HIS A 330 "
        pdb=" CG  HIS A 330 "
        pdb=" CD2 HIS A 330 "
      ideal   model   delta    sigma   weight residual
     131.20  125.26    5.94 1.30e+00 5.92e-01 2.09e+01
  angle pdb=" CB  HIS C 330 "
        pdb=" CG  HIS C 330 "
        pdb=" CD2 HIS C 330 "
      ideal   model   delta    sigma   weight residual
     131.20  125.36    5.84 1.30e+00 5.92e-01 2.02e+01
  ... (remaining 12907 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.25: 2901
       14.25 -    28.49: 173
       28.49 -    42.73: 69
       42.73 -    56.98: 58
       56.98 -    71.22: 63
  Dihedral angle restraints: 3264
    sinusoidal: 1866
      harmonic: 1398
  Sorted by residual:
  dihedral pdb=" CA  ASP F 358 "
           pdb=" C   ASP F 358 "
           pdb=" N   ASN F 359 "
           pdb=" CA  ASN F 359 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.44   19.56     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  ASP E 358 "
           pdb=" C   ASP E 358 "
           pdb=" N   ASN E 359 "
           pdb=" CA  ASN E 359 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.42   18.58     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  GLY A 333 "
           pdb=" C   GLY A 333 "
           pdb=" N   GLY A 334 "
           pdb=" CA  GLY A 334 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.60   18.40     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 3261 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 273
       0.061 -    0.121: 182
       0.121 -    0.181: 57
       0.181 -    0.241: 13
       0.241 -    0.302: 3
  Chirality restraints: 528
  Sorted by residual:
  chirality pdb=" CA  LYS C 347 "
            pdb=" N   LYS C 347 "
            pdb=" C   LYS C 347 "
            pdb=" CB  LYS C 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.28e+00
  chirality pdb=" CA  LYS A 347 "
            pdb=" N   LYS A 347 "
            pdb=" C   LYS A 347 "
            pdb=" CB  LYS A 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.53e+00
  chirality pdb=" CA  ASP B 348 "
            pdb=" N   ASP B 348 "
            pdb=" C   ASP B 348 "
            pdb=" CB  ASP B 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.50e+00
  ... (remaining 525 not shown)

  Planarity restraints: 1020
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 310 "    0.097 2.00e-02 2.50e+03   4.22e-02 5.33e+01
        pdb=" CG  TYR A 310 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 310 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 310 "   -0.031 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 310 "   -0.035 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 310 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 310 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR A 310 "    0.073 2.00e-02 2.50e+03
        pdb=" HD1 TYR A 310 "    0.004 2.00e-02 2.50e+03
        pdb=" HD2 TYR A 310 "   -0.051 2.00e-02 2.50e+03
        pdb=" HE1 TYR A 310 "   -0.028 2.00e-02 2.50e+03
        pdb=" HE2 TYR A 310 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS F 330 "   -0.083 2.00e-02 2.50e+03   4.61e-02 4.79e+01
        pdb=" CG  HIS F 330 "    0.048 2.00e-02 2.50e+03
        pdb=" ND1 HIS F 330 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 HIS F 330 "    0.053 2.00e-02 2.50e+03
        pdb=" CE1 HIS F 330 "    0.015 2.00e-02 2.50e+03
        pdb=" NE2 HIS F 330 "    0.023 2.00e-02 2.50e+03
        pdb=" HD2 HIS F 330 "    0.011 2.00e-02 2.50e+03
        pdb=" HE1 HIS F 330 "   -0.022 2.00e-02 2.50e+03
        pdb=" HE2 HIS F 330 "   -0.071 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS E 362 "   -0.064 2.00e-02 2.50e+03   3.80e-02 3.24e+01
        pdb=" CG  HIS E 362 "    0.053 2.00e-02 2.50e+03
        pdb=" ND1 HIS E 362 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 HIS E 362 "    0.047 2.00e-02 2.50e+03
        pdb=" CE1 HIS E 362 "    0.013 2.00e-02 2.50e+03
        pdb=" NE2 HIS E 362 "    0.024 2.00e-02 2.50e+03
        pdb=" HD2 HIS E 362 "   -0.010 2.00e-02 2.50e+03
        pdb=" HE1 HIS E 362 "   -0.024 2.00e-02 2.50e+03
        pdb=" HE2 HIS E 362 "   -0.049 2.00e-02 2.50e+03
  ... (remaining 1017 not shown)

  Histogram of nonbonded interaction distances:
        1.55 -     2.16: 461
        2.16 -     2.77: 11796
        2.77 -     3.38: 18028
        3.38 -     3.99: 24413
        3.99 -     4.60: 33930
  Nonbonded interactions: 88628
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 314 "
            pdb=" HG  SER A 316 "
     model   vdw
     1.547 2.450
  nonbonded pdb=" OD1 ASP F 314 "
            pdb=" HG  SER F 316 "
     model   vdw
     1.559 2.450
  nonbonded pdb=" OD1 ASP C 314 "
            pdb=" HG  SER C 316 "
     model   vdw
     1.563 2.450
  nonbonded pdb=" OD1 ASP D 314 "
            pdb=" HG  SER D 316 "
     model   vdw
     1.572 2.450
  nonbonded pdb=" OD1 ASP E 314 "
            pdb=" HG  SER E 316 "
     model   vdw
     1.605 2.450
  ... (remaining 88623 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:             2.230
  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:             0.110
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     19.340
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
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   0.035   3498  Z= 0.726
  Angle     :  1.800   6.925   4680  Z= 1.189
  Chirality :  0.083   0.302    528
  Planarity :  0.010   0.083    594
  Dihedral  :  9.918  46.311   1344
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  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: -1.95 (0.34), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.48 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.003   HIS D 329 
 PHE   0.049   0.013   PHE E 346 
 TYR   0.084   0.016   TYR A 310 
 ARG   0.007   0.001   ARG E 349 

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.602 
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: symmetry clash
REVERT: E  311 LYS cc_start: 0.7839 (mttt) cc_final: 0.7228 (pttp)
REVERT: E  347 LYS cc_start: 0.8576 (mttt) cc_final: 0.7816 (mtmt)
REVERT: E  369 LYS cc_start: 0.8128 (tttt) cc_final: 0.7668 (ttmm)
REVERT: E  371 ILE cc_start: 0.8679 (mt) cc_final: 0.8055 (mt)
REVERT: A  307 GLN cc_start: 0.6964 (tt0) cc_final: 0.6477 (mt0)
REVERT: A  338 GLU cc_start: 0.6756 (tt0) cc_final: 0.6217 (tm-30)
REVERT: A  369 LYS cc_start: 0.7458 (tttt) cc_final: 0.7171 (ttpp)
REVERT: A  375 LYS cc_start: 0.7396 (tttt) cc_final: 0.7091 (tttt)
REVERT: F  307 GLN cc_start: 0.7165 (tt0) cc_final: 0.6604 (mt0)
REVERT: F  317 LYS cc_start: 0.6801 (mttt) cc_final: 0.6299 (mtpt)
REVERT: F  338 GLU cc_start: 0.6879 (tt0) cc_final: 0.6548 (tm-30)
REVERT: F  340 LYS cc_start: 0.7139 (tttt) cc_final: 0.6616 (mttm)
REVERT: F  369 LYS cc_start: 0.7165 (tttt) cc_final: 0.6629 (ttmm)
REVERT: F  371 ILE cc_start: 0.7782 (mt) cc_final: 0.7524 (mp)
REVERT: B  307 GLN cc_start: 0.8218 (tt0) cc_final: 0.7395 (mt0)
REVERT: B  317 LYS cc_start: 0.8017 (mttt) cc_final: 0.7306 (mtpt)
REVERT: B  340 LYS cc_start: 0.8242 (tttt) cc_final: 0.7388 (ttmt)
REVERT: B  353 LYS cc_start: 0.7157 (mttt) cc_final: 0.6773 (tttm)
REVERT: B  369 LYS cc_start: 0.8225 (tttt) cc_final: 0.7650 (tttp)
REVERT: C  311 LYS cc_start: 0.7575 (mttt) cc_final: 0.7343 (mttm)
REVERT: C  317 LYS cc_start: 0.6972 (mttt) cc_final: 0.6681 (mtpp)
REVERT: C  338 GLU cc_start: 0.7053 (tt0) cc_final: 0.6821 (tt0)
REVERT: C  369 LYS cc_start: 0.7752 (tttt) cc_final: 0.7348 (tttp)
REVERT: D  307 GLN cc_start: 0.7497 (tt0) cc_final: 0.7266 (tt0)
REVERT: D  311 LYS cc_start: 0.7490 (mttt) cc_final: 0.7202 (mtmt)
REVERT: D  317 LYS cc_start: 0.6932 (mttt) cc_final: 0.6344 (mtpp)
REVERT: D  340 LYS cc_start: 0.7267 (tttt) cc_final: 0.6595 (ttmt)
REVERT: D  369 LYS cc_start: 0.7547 (tttt) cc_final: 0.7034 (tttp)
REVERT: D  372 GLU cc_start: 0.7486 (tt0) cc_final: 0.7270 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.6854
  time to fit residues: 97.0010
Evaluate side-chains
  85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 17 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 12 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
E 327 ASN
B 327 ASN
B 330 HIS
D 351 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.129829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.114077 restraints weight = 13555.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3796 rms_B_bonded: 1.96
r_work: 0.3727 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3646 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.3692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3498  Z= 0.276
  Angle     :  0.599   4.992   4680  Z= 0.310
  Chirality :  0.052   0.137    528
  Planarity :  0.003   0.025    594
  Dihedral  :  5.921  14.474    462
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 1.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  5.05 %
    Favored  : 93.94 %
  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: -1.18 (0.38), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.89 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B 330 
 PHE   0.010   0.002   PHE C 346 
 TYR   0.010   0.003   TYR B 310 
 ARG   0.004   0.001   ARG E 379 

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.647 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  314 ASP cc_start: 0.8235 (t0) cc_final: 0.7711 (t0)
REVERT: E  369 LYS cc_start: 0.8464 (tttt) cc_final: 0.8111 (ttmm)
REVERT: A  307 GLN cc_start: 0.7662 (tt0) cc_final: 0.7316 (mt0)
REVERT: A  311 LYS cc_start: 0.8123 (mttt) cc_final: 0.7516 (tttt)
REVERT: A  317 LYS cc_start: 0.7780 (mttt) cc_final: 0.7435 (mtpt)
REVERT: A  338 GLU cc_start: 0.7557 (tt0) cc_final: 0.7257 (tm-30)
REVERT: A  369 LYS cc_start: 0.8275 (tttt) cc_final: 0.7921 (ttmm)
REVERT: F  307 GLN cc_start: 0.7895 (tt0) cc_final: 0.7458 (mt0)
REVERT: F  311 LYS cc_start: 0.8297 (mttt) cc_final: 0.7680 (pttp)
REVERT: F  342 GLU cc_start: 0.6819 (mp0) cc_final: 0.6590 (mp0)
REVERT: F  348 ASP cc_start: 0.8496 (t0) cc_final: 0.8271 (t0)
REVERT: B  317 LYS cc_start: 0.8246 (mttt) cc_final: 0.7798 (mtpt)
REVERT: B  340 LYS cc_start: 0.8368 (tttt) cc_final: 0.8077 (ttmt)
REVERT: B  369 LYS cc_start: 0.8492 (tttt) cc_final: 0.8064 (tttp)
REVERT: C  307 GLN cc_start: 0.8203 (tt0) cc_final: 0.7917 (tt0)
REVERT: C  311 LYS cc_start: 0.8233 (mttt) cc_final: 0.7962 (mttm)
REVERT: C  317 LYS cc_start: 0.8075 (mttt) cc_final: 0.7818 (mtpp)
REVERT: C  338 GLU cc_start: 0.7872 (tt0) cc_final: 0.7640 (tt0)
REVERT: C  340 LYS cc_start: 0.7914 (tttt) cc_final: 0.7287 (mttm)
REVERT: C  369 LYS cc_start: 0.8439 (tttt) cc_final: 0.8119 (tttp)
REVERT: D  311 LYS cc_start: 0.8358 (mttt) cc_final: 0.8113 (mtmt)
REVERT: D  317 LYS cc_start: 0.7927 (mttt) cc_final: 0.7462 (mtpp)
REVERT: D  340 LYS cc_start: 0.7916 (tttt) cc_final: 0.7287 (mttm)
REVERT: D  369 LYS cc_start: 0.8354 (tttt) cc_final: 0.7919 (tttp)
  outliers start: 4
  outliers final: 4
  residues processed: 87
  average time/residue: 0.6883
  time to fit residues: 65.8885
Evaluate side-chains
  76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain F residue  305 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 21 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   chunk 12 optimal weight:    4.9990
   chunk 36 optimal weight:    8.9990
   chunk 18 optimal weight:    8.9990
   chunk 11 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   overall best weight:    2.1188

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.130376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.115804 restraints weight = 13260.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3786 rms_B_bonded: 1.88
r_work: 0.3717 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3636 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.4357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3498  Z= 0.203
  Angle     :  0.528   4.966   4680  Z= 0.269
  Chirality :  0.052   0.133    528
  Planarity :  0.003   0.020    594
  Dihedral  :  5.212  12.799    462
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 1.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  6.06 %
    Favored  : 92.17 %
  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: -0.99 (0.39), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.74 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 329 
 PHE   0.006   0.001   PHE F 346 
 TYR   0.010   0.002   TYR A 310 
 ARG   0.001   0.000   ARG B 349 

*********************** 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
  80 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  369 LYS cc_start: 0.8431 (tttt) cc_final: 0.8091 (ttmm)
REVERT: A  307 GLN cc_start: 0.7711 (tt0) cc_final: 0.7338 (mt0)
REVERT: A  311 LYS cc_start: 0.8139 (mttt) cc_final: 0.7527 (tttt)
REVERT: A  317 LYS cc_start: 0.7869 (mttt) cc_final: 0.7508 (mtpt)
REVERT: A  338 GLU cc_start: 0.7625 (tt0) cc_final: 0.7330 (tm-30)
REVERT: A  347 LYS cc_start: 0.8691 (mttt) cc_final: 0.8261 (mtpp)
REVERT: A  369 LYS cc_start: 0.8228 (tttt) cc_final: 0.7903 (ttmm)
REVERT: F  307 GLN cc_start: 0.7922 (tt0) cc_final: 0.7479 (mt0)
REVERT: F  311 LYS cc_start: 0.8274 (mttt) cc_final: 0.7687 (pttt)
REVERT: F  342 GLU cc_start: 0.6935 (mp0) cc_final: 0.6662 (mp0)
REVERT: B  317 LYS cc_start: 0.8212 (mttt) cc_final: 0.7812 (mtpt)
REVERT: B  340 LYS cc_start: 0.8428 (tttt) cc_final: 0.7729 (mttm)
REVERT: B  369 LYS cc_start: 0.8432 (tttt) cc_final: 0.8102 (tttp)
REVERT: C  307 GLN cc_start: 0.8228 (tt0) cc_final: 0.7949 (tt0)
REVERT: C  317 LYS cc_start: 0.8127 (mttt) cc_final: 0.7857 (mtpp)
REVERT: C  338 GLU cc_start: 0.7787 (tt0) cc_final: 0.7510 (tt0)
REVERT: C  369 LYS cc_start: 0.8409 (tttt) cc_final: 0.8105 (tttp)
REVERT: D  311 LYS cc_start: 0.8331 (mttt) cc_final: 0.8086 (mtmt)
REVERT: D  317 LYS cc_start: 0.7904 (mttt) cc_final: 0.7484 (mtpp)
REVERT: D  351 GLN cc_start: 0.7668 (tt0) cc_final: 0.6988 (mt0)
REVERT: D  369 LYS cc_start: 0.8331 (tttt) cc_final: 0.7912 (tttp)
  outliers start: 7
  outliers final: 6
  residues processed: 80
  average time/residue: 0.6851
  time to fit residues: 60.7103
Evaluate side-chains
  73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain F residue  305 SER
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain D residue  324 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 37 optimal weight:    7.9990
   chunk 10 optimal weight:    7.9990
   chunk 12 optimal weight:    3.9990
   chunk 40 optimal weight:    0.2980
   chunk 35 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 14 optimal weight:    7.9990
   chunk 21 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   overall best weight:    1.2982

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

Flipped N/Q/H residues before XYZ refinement:
B 368 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.136691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.122827 restraints weight = 12749.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3850 rms_B_bonded: 1.77
r_work: 0.3784 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.3705 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.4690

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= 0.149
  Angle     :  0.478   4.952   4680  Z= 0.241
  Chirality :  0.051   0.132    528
  Planarity :  0.002   0.019    594
  Dihedral  :  4.810  12.540    462
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 0.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  7.32 %
    Favored  : 91.16 %
  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: -0.81 (0.40), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.61 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS C 329 
 PHE   0.004   0.001   PHE B 346 
 TYR   0.006   0.001   TYR F 310 
 ARG   0.002   0.000   ARG A 349 

*********************** 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
  82 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.555 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  369 LYS cc_start: 0.8406 (tttt) cc_final: 0.8090 (ttmm)
REVERT: A  307 GLN cc_start: 0.7718 (tt0) cc_final: 0.7411 (mt0)
REVERT: A  311 LYS cc_start: 0.8122 (mttt) cc_final: 0.7503 (tttt)
REVERT: A  315 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8519 (mt)
REVERT: A  317 LYS cc_start: 0.7866 (mttt) cc_final: 0.7524 (mtpt)
REVERT: A  338 GLU cc_start: 0.7626 (tt0) cc_final: 0.7359 (tm-30)
REVERT: A  347 LYS cc_start: 0.8698 (mttt) cc_final: 0.8391 (mtpp)
REVERT: A  369 LYS cc_start: 0.8182 (tttt) cc_final: 0.7878 (ttmm)
REVERT: F  307 GLN cc_start: 0.7878 (tt0) cc_final: 0.7491 (mt0)
REVERT: F  341 SER cc_start: 0.8700 (m) cc_final: 0.8288 (m)
REVERT: F  342 GLU cc_start: 0.6963 (mp0) cc_final: 0.6627 (mp0)
REVERT: F  369 LYS cc_start: 0.8307 (tttt) cc_final: 0.7879 (ttmm)
REVERT: B  317 LYS cc_start: 0.8097 (mttt) cc_final: 0.7644 (mtpp)
REVERT: B  340 LYS cc_start: 0.8277 (tttt) cc_final: 0.7745 (mttm)
REVERT: B  369 LYS cc_start: 0.8533 (tttt) cc_final: 0.8210 (tttp)
REVERT: C  307 GLN cc_start: 0.8249 (tt0) cc_final: 0.7988 (tt0)
REVERT: C  338 GLU cc_start: 0.7792 (tt0) cc_final: 0.7587 (tt0)
REVERT: C  369 LYS cc_start: 0.8402 (tttt) cc_final: 0.8118 (tttp)
REVERT: D  311 LYS cc_start: 0.8314 (mttt) cc_final: 0.8080 (mtmt)
REVERT: D  317 LYS cc_start: 0.7948 (mttt) cc_final: 0.7556 (mtpp)
REVERT: D  351 GLN cc_start: 0.7686 (tt0) cc_final: 0.7038 (mt0)
REVERT: D  369 LYS cc_start: 0.8318 (tttt) cc_final: 0.7908 (tttp)
  outliers start: 6
  outliers final: 3
  residues processed: 81
  average time/residue: 0.6396
  time to fit residues: 57.4712
Evaluate side-chains
  69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain D residue  324 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   chunk 38 optimal weight:   10.0000
   chunk 30 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 4 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
D 327 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.132018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.117840 restraints weight = 12739.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3753 rms_B_bonded: 1.78
r_work: 0.3685 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3604 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.4852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   3498  Z= 0.270
  Angle     :  0.522   4.665   4680  Z= 0.267
  Chirality :  0.050   0.133    528
  Planarity :  0.003   0.020    594
  Dihedral  :  4.954  13.006    462
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 1.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  :  7.32 %
    Favored  : 89.90 %
  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: -0.84 (0.40), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.63 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 329 
 PHE   0.006   0.001   PHE B 346 
 TYR   0.010   0.002   TYR A 310 
 ARG   0.002   0.000   ARG C 379 

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.622 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  369 LYS cc_start: 0.8398 (tttt) cc_final: 0.8045 (ttmm)
REVERT: A  307 GLN cc_start: 0.7683 (tt0) cc_final: 0.7262 (mt0)
REVERT: A  315 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8547 (mt)
REVERT: A  317 LYS cc_start: 0.7866 (mttt) cc_final: 0.7465 (mtpt)
REVERT: A  338 GLU cc_start: 0.7654 (tt0) cc_final: 0.7303 (tm-30)
REVERT: A  347 LYS cc_start: 0.8610 (mttt) cc_final: 0.8263 (mtpp)
REVERT: A  369 LYS cc_start: 0.8171 (tttt) cc_final: 0.7843 (ttmm)
REVERT: A  372 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7159 (tm-30)
REVERT: F  307 GLN cc_start: 0.7892 (tt0) cc_final: 0.7390 (mt0)
REVERT: F  311 LYS cc_start: 0.8219 (mttt) cc_final: 0.7534 (pttt)
REVERT: F  342 GLU cc_start: 0.6880 (mp0) cc_final: 0.6588 (mp0)
REVERT: F  369 LYS cc_start: 0.8283 (tttt) cc_final: 0.7825 (ttmm)
REVERT: B  317 LYS cc_start: 0.8326 (mttt) cc_final: 0.7864 (mtpp)
REVERT: B  340 LYS cc_start: 0.8348 (tttt) cc_final: 0.7754 (mttm)
REVERT: B  369 LYS cc_start: 0.8635 (tttt) cc_final: 0.8295 (tttp)
REVERT: C  307 GLN cc_start: 0.8223 (tt0) cc_final: 0.7960 (tt0)
REVERT: C  338 GLU cc_start: 0.7729 (tt0) cc_final: 0.7389 (tt0)
REVERT: D  311 LYS cc_start: 0.8294 (mttt) cc_final: 0.7996 (mtmt)
REVERT: D  317 LYS cc_start: 0.7985 (mttt) cc_final: 0.7533 (mtpp)
REVERT: D  338 GLU cc_start: 0.7879 (tt0) cc_final: 0.7653 (tt0)
REVERT: D  369 LYS cc_start: 0.8319 (tttt) cc_final: 0.7854 (tttp)
  outliers start: 11
  outliers final: 9
  residues processed: 77
  average time/residue: 0.5839
  time to fit residues: 50.6004
Evaluate side-chains
  76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain F residue  305 SER
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain D residue  324 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 = 0.3967 r_free = 0.3967 target = 0.133484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.119567 restraints weight = 12813.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3796 rms_B_bonded: 1.78
r_work: 0.3727 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.3644 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.4975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3498  Z= 0.199
  Angle     :  0.488   4.944   4680  Z= 0.248
  Chirality :  0.051   0.133    528
  Planarity :  0.003   0.020    594
  Dihedral  :  4.772  11.674    462
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 1.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  :  8.08 %
    Favored  : 89.39 %
  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: -0.87 (0.40), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.65 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS C 329 
 PHE   0.004   0.001   PHE B 346 
 TYR   0.007   0.002   TYR A 310 
 ARG   0.001   0.000   ARG F 379 

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  369 LYS cc_start: 0.8413 (tttt) cc_final: 0.8073 (ttmm)
REVERT: A  307 GLN cc_start: 0.7734 (tt0) cc_final: 0.7365 (mt0)
REVERT: A  311 LYS cc_start: 0.8211 (mttt) cc_final: 0.7574 (tttt)
REVERT: A  315 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8605 (mt)
REVERT: A  317 LYS cc_start: 0.7900 (mttt) cc_final: 0.7519 (mtpt)
REVERT: A  338 GLU cc_start: 0.7642 (tt0) cc_final: 0.7345 (tm-30)
REVERT: A  347 LYS cc_start: 0.8654 (mttt) cc_final: 0.8333 (mtpp)
REVERT: A  369 LYS cc_start: 0.8203 (tttt) cc_final: 0.7868 (ttmm)
REVERT: A  372 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7116 (tm-30)
REVERT: F  307 GLN cc_start: 0.7914 (tt0) cc_final: 0.7558 (mt0)
REVERT: F  311 LYS cc_start: 0.8264 (mttt) cc_final: 0.7667 (pttt)
REVERT: F  369 LYS cc_start: 0.8334 (tttt) cc_final: 0.7905 (ttmm)
REVERT: B  317 LYS cc_start: 0.8304 (mttt) cc_final: 0.7904 (mtpp)
REVERT: B  340 LYS cc_start: 0.8339 (tttt) cc_final: 0.7674 (mttm)
REVERT: B  342 GLU cc_start: 0.7353 (mp0) cc_final: 0.7150 (mp0)
REVERT: B  369 LYS cc_start: 0.8600 (tttt) cc_final: 0.8317 (tttp)
REVERT: C  307 GLN cc_start: 0.8269 (tt0) cc_final: 0.8012 (tt0)
REVERT: D  311 LYS cc_start: 0.8335 (mttt) cc_final: 0.8060 (mtmt)
REVERT: D  317 LYS cc_start: 0.8000 (mttt) cc_final: 0.7585 (mtpp)
REVERT: D  369 LYS cc_start: 0.8349 (tttt) cc_final: 0.7918 (tttp)
  outliers start: 10
  outliers final: 8
  residues processed: 76
  average time/residue: 0.5813
  time to fit residues: 49.5704
Evaluate side-chains
  76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain F residue  305 SER
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain D residue  324 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 38 optimal weight:    7.9990
   chunk 12 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 11 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
B 368 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.130497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.115782 restraints weight = 13308.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3801 rms_B_bonded: 1.91
r_work: 0.3728 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3641 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.5066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3498  Z= 0.180
  Angle     :  0.480   4.776   4680  Z= 0.244
  Chirality :  0.051   0.132    528
  Planarity :  0.002   0.019    594
  Dihedral  :  4.634  11.241    462
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 1.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  :  8.84 %
    Favored  : 88.64 %
  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: -0.86 (0.39), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.65 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS C 329 
 PHE   0.004   0.001   PHE B 346 
 TYR   0.007   0.002   TYR A 310 
 ARG   0.001   0.000   ARG E 379 

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  369 LYS cc_start: 0.8419 (tttt) cc_final: 0.8076 (ttmm)
REVERT: A  307 GLN cc_start: 0.7742 (tt0) cc_final: 0.7334 (mt0)
REVERT: A  311 LYS cc_start: 0.8192 (mttt) cc_final: 0.7515 (tttt)
REVERT: A  315 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8570 (mt)
REVERT: A  317 LYS cc_start: 0.7848 (mttt) cc_final: 0.7480 (mtpt)
REVERT: A  338 GLU cc_start: 0.7617 (tt0) cc_final: 0.7281 (tm-30)
REVERT: A  347 LYS cc_start: 0.8675 (mttt) cc_final: 0.8333 (mtpp)
REVERT: A  369 LYS cc_start: 0.8216 (tttt) cc_final: 0.7884 (ttmm)
REVERT: A  372 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7138 (tm-30)
REVERT: F  307 GLN cc_start: 0.7889 (tt0) cc_final: 0.7529 (mt0)
REVERT: F  311 LYS cc_start: 0.8231 (mttt) cc_final: 0.7599 (pttt)
REVERT: F  369 LYS cc_start: 0.8335 (tttt) cc_final: 0.7895 (ttmm)
REVERT: B  317 LYS cc_start: 0.8301 (mttt) cc_final: 0.7918 (mtpp)
REVERT: B  340 LYS cc_start: 0.8356 (tttt) cc_final: 0.7644 (mttm)
REVERT: B  342 GLU cc_start: 0.7376 (mp0) cc_final: 0.7116 (mp0)
REVERT: B  369 LYS cc_start: 0.8637 (tttt) cc_final: 0.8346 (tttp)
REVERT: C  307 GLN cc_start: 0.8264 (tt0) cc_final: 0.8011 (tt0)
REVERT: D  311 LYS cc_start: 0.8309 (mttt) cc_final: 0.8013 (mtmt)
REVERT: D  317 LYS cc_start: 0.7979 (mttt) cc_final: 0.7580 (mtpp)
  outliers start: 10
  outliers final: 8
  residues processed: 74
  average time/residue: 0.6039
  time to fit residues: 50.4815
Evaluate side-chains
  73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain F residue  305 SER
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain D residue  324 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:    7.9990
   chunk 38 optimal weight:    7.9990
   chunk 15 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 17 optimal weight:    8.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
B 368 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.132502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.118496 restraints weight = 12931.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.3781 rms_B_bonded: 1.78
r_work: 0.3713 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.3631 rms_B_bonded: 2.97 restraints_weight: 0.2500
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.5135

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= 0.216
  Angle     :  0.489   4.634   4680  Z= 0.249
  Chirality :  0.050   0.132    528
  Planarity :  0.003   0.019    594
  Dihedral  :  4.691  11.365    462
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 1.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  :  8.84 %
    Favored  : 88.64 %
  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: -0.93 (0.39), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.70 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS C 329 
 PHE   0.005   0.001   PHE E 378 
 TYR   0.009   0.002   TYR F 310 
 ARG   0.001   0.000   ARG B 379 

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  369 LYS cc_start: 0.8426 (tttt) cc_final: 0.8095 (ttmm)
REVERT: A  307 GLN cc_start: 0.7700 (tt0) cc_final: 0.7332 (mt0)
REVERT: A  311 LYS cc_start: 0.8236 (mttt) cc_final: 0.7585 (tttt)
REVERT: A  315 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8636 (mt)
REVERT: A  317 LYS cc_start: 0.7904 (mttt) cc_final: 0.7531 (mtpt)
REVERT: A  338 GLU cc_start: 0.7622 (tt0) cc_final: 0.7316 (tm-30)
REVERT: A  347 LYS cc_start: 0.8686 (mttt) cc_final: 0.8360 (mtpp)
REVERT: A  369 LYS cc_start: 0.8277 (tttt) cc_final: 0.7944 (ttmm)
REVERT: A  372 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7127 (tm-30)
REVERT: F  307 GLN cc_start: 0.7873 (tt0) cc_final: 0.7555 (mt0)
REVERT: F  311 LYS cc_start: 0.8254 (mttt) cc_final: 0.7643 (pttt)
REVERT: F  369 LYS cc_start: 0.8335 (tttt) cc_final: 0.7925 (ttmm)
REVERT: B  317 LYS cc_start: 0.8330 (mttt) cc_final: 0.7990 (mtpp)
REVERT: B  340 LYS cc_start: 0.8397 (tttt) cc_final: 0.7694 (mttm)
REVERT: B  351 GLN cc_start: 0.7865 (tt0) cc_final: 0.7437 (mt0)
REVERT: B  369 LYS cc_start: 0.8610 (tttt) cc_final: 0.8319 (tttp)
REVERT: C  307 GLN cc_start: 0.8244 (tt0) cc_final: 0.7998 (tt0)
REVERT: D  311 LYS cc_start: 0.8335 (mttt) cc_final: 0.8064 (mtmt)
REVERT: D  317 LYS cc_start: 0.7993 (mttt) cc_final: 0.7618 (mtpp)
REVERT: D  369 LYS cc_start: 0.8409 (tttt) cc_final: 0.7969 (tttp)
REVERT: D  379 ARG cc_start: 0.7160 (mtp85) cc_final: 0.6921 (mtp85)
  outliers start: 10
  outliers final: 8
  residues processed: 76
  average time/residue: 0.6057
  time to fit residues: 51.4107
Evaluate side-chains
  76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain D residue  324 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 40 optimal weight:    7.9990
   chunk 29 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
B 368 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.133321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.119462 restraints weight = 12851.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3796 rms_B_bonded: 1.78
r_work: 0.3728 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.3645 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.5174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3498  Z= 0.187
  Angle     :  0.489   5.209   4680  Z= 0.249
  Chirality :  0.050   0.133    528
  Planarity :  0.002   0.019    594
  Dihedral  :  4.580  12.061    462
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 1.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  :  9.09 %
    Favored  : 88.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.40), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.68 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS C 329 
 PHE   0.004   0.001   PHE E 378 
 TYR   0.007   0.002   TYR A 310 
 ARG   0.001   0.000   ARG B 349 

*********************** 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
  81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  347 LYS cc_start: 0.8788 (mttt) cc_final: 0.8349 (mtpp)
REVERT: E  369 LYS cc_start: 0.8418 (tttt) cc_final: 0.8083 (ttmm)
REVERT: A  307 GLN cc_start: 0.7708 (tt0) cc_final: 0.7341 (mt0)
REVERT: A  311 LYS cc_start: 0.8207 (mttt) cc_final: 0.7560 (tttt)
REVERT: A  315 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8605 (mt)
REVERT: A  317 LYS cc_start: 0.7872 (mttt) cc_final: 0.7510 (mtpt)
REVERT: A  338 GLU cc_start: 0.7627 (tt0) cc_final: 0.7309 (tm-30)
REVERT: A  347 LYS cc_start: 0.8689 (mttt) cc_final: 0.8358 (mtpp)
REVERT: A  369 LYS cc_start: 0.8256 (tttt) cc_final: 0.7927 (ttmm)
REVERT: A  372 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7093 (tm-30)
REVERT: F  307 GLN cc_start: 0.7864 (tt0) cc_final: 0.7556 (mt0)
REVERT: F  311 LYS cc_start: 0.8235 (mttt) cc_final: 0.7618 (pttt)
REVERT: F  351 GLN cc_start: 0.7905 (tt0) cc_final: 0.7542 (mt0)
REVERT: F  369 LYS cc_start: 0.8321 (tttt) cc_final: 0.7911 (ttmm)
REVERT: B  317 LYS cc_start: 0.8279 (mttt) cc_final: 0.7954 (mtpp)
REVERT: B  340 LYS cc_start: 0.8366 (tttt) cc_final: 0.7748 (mttm)
REVERT: B  351 GLN cc_start: 0.7895 (tt0) cc_final: 0.7463 (mt0)
REVERT: B  369 LYS cc_start: 0.8607 (tttt) cc_final: 0.8334 (tttp)
REVERT: C  307 GLN cc_start: 0.8251 (tt0) cc_final: 0.7995 (tt0)
REVERT: D  311 LYS cc_start: 0.8326 (mttt) cc_final: 0.8019 (mtmm)
REVERT: D  317 LYS cc_start: 0.7947 (mttt) cc_final: 0.7587 (mtpp)
REVERT: D  379 ARG cc_start: 0.7094 (mtp85) cc_final: 0.6872 (mtp85)
  outliers start: 10
  outliers final: 8
  residues processed: 80
  average time/residue: 0.6559
  time to fit residues: 58.5921
Evaluate side-chains
  79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain D residue  324 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   chunk 18 optimal weight:    0.8980
   chunk 17 optimal weight:    6.9990
   chunk 8 optimal weight:    5.9990
   chunk 6 optimal weight:    0.6980
   chunk 31 optimal weight:    6.9990
   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 = 0.3970 r_free = 0.3970 target = 0.133617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.119692 restraints weight = 13005.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3799 rms_B_bonded: 1.79
r_work: 0.3730 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.3647 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.5241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3498  Z= 0.184
  Angle     :  0.485   4.669   4680  Z= 0.247
  Chirality :  0.050   0.130    528
  Planarity :  0.003   0.018    594
  Dihedral  :  4.543  11.378    462
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 1.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  :  9.34 %
    Favored  : 88.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.40), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.69 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS C 329 
 PHE   0.005   0.001   PHE B 346 
 TYR   0.007   0.002   TYR A 310 
 ARG   0.001   0.000   ARG A 379 

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  347 LYS cc_start: 0.8786 (mttt) cc_final: 0.8348 (mtpp)
REVERT: E  369 LYS cc_start: 0.8411 (tttt) cc_final: 0.8076 (ttmm)
REVERT: A  307 GLN cc_start: 0.7705 (tt0) cc_final: 0.7331 (mt0)
REVERT: A  311 LYS cc_start: 0.8255 (mttt) cc_final: 0.7583 (tttt)
REVERT: A  315 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8613 (mt)
REVERT: A  317 LYS cc_start: 0.7872 (mttt) cc_final: 0.7517 (mtpt)
REVERT: A  338 GLU cc_start: 0.7640 (tt0) cc_final: 0.7320 (tm-30)
REVERT: A  347 LYS cc_start: 0.8694 (mttt) cc_final: 0.8364 (mtpp)
REVERT: A  369 LYS cc_start: 0.8227 (tttt) cc_final: 0.7902 (ttmm)
REVERT: A  372 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7123 (tm-30)
REVERT: F  307 GLN cc_start: 0.7871 (tt0) cc_final: 0.7566 (mt0)
REVERT: F  311 LYS cc_start: 0.8241 (mttt) cc_final: 0.7624 (pttt)
REVERT: F  351 GLN cc_start: 0.7917 (tt0) cc_final: 0.7545 (mt0)
REVERT: F  369 LYS cc_start: 0.8330 (tttt) cc_final: 0.7922 (ttmm)
REVERT: B  317 LYS cc_start: 0.8290 (mttt) cc_final: 0.7991 (mtpp)
REVERT: B  340 LYS cc_start: 0.8363 (tttt) cc_final: 0.7953 (ttmt)
REVERT: B  351 GLN cc_start: 0.7902 (tt0) cc_final: 0.7484 (mt0)
REVERT: B  369 LYS cc_start: 0.8598 (tttt) cc_final: 0.8327 (tttp)
REVERT: C  307 GLN cc_start: 0.8252 (tt0) cc_final: 0.7992 (tt0)
REVERT: D  311 LYS cc_start: 0.8306 (mttt) cc_final: 0.8000 (mtmm)
REVERT: D  317 LYS cc_start: 0.7997 (mttt) cc_final: 0.7632 (mtpp)
  outliers start: 9
  outliers final: 7
  residues processed: 78
  average time/residue: 0.6233
  time to fit residues: 54.4123
Evaluate side-chains
  78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain D residue  324 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 41 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 36 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 4 optimal weight:    0.0270
   chunk 8 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    1.1844

-------------------------------------------------------------------------------
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 = 0.3961 r_free = 0.3961 target = 0.126811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.112125 restraints weight = 13715.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3805 rms_B_bonded: 1.93
r_work: 0.3731 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3646 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.5302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3498  Z= 0.148
  Angle     :  0.468   4.635   4680  Z= 0.238
  Chirality :  0.051   0.131    528
  Planarity :  0.002   0.018    594
  Dihedral  :  4.392  11.069    462
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 1.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 10.10 %
    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 (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: -0.87 (0.40), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.65 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS C 362 
 PHE   0.003   0.001   PHE B 346 
 TYR   0.005   0.001   TYR F 310 
 ARG   0.004   0.000   ARG D 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4682.11 seconds
wall clock time: 80 minutes 19.97 seconds (4819.97 seconds total)