Starting phenix.real_space_refine
on Wed Feb 12 02:55:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q9d_18277/02_2025/8q9d_18277.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q9d_18277/02_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_18277/02_2025/8q9d_18277.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q9d_18277/02_2025/8q9d_18277.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q9d_18277/02_2025/8q9d_18277.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q9d_18277/02_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7032
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "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: 4.84, per 1000 atoms: 0.69
  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: 1.51
  Conformation dependent library (CDL) restraints added in 631.9 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: 0.70
  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: 2.30

  Time building geometry restraints manager: 1.88 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:             3.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.120
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     19.710
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.140
-------------------------------------------------------------------------------
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  : 0.580 
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: 0.7063
  time to fit residues: 100.0530
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  : 0.611 
-------------------------------------------------------------------------------
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:    3.9990
   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 = 32)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.114069 restraints weight = 13555.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3796 rms_B_bonded: 1.96
r_work: 0.3727 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3645 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3645
-------------------------------------------------------------------------------
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  : 0.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  314 ASP cc_start: 0.8237 (t0) cc_final: 0.7713 (t0)
REVERT: E  369 LYS cc_start: 0.8464 (tttt) cc_final: 0.8111 (ttmm)
REVERT: A  307 GLN cc_start: 0.7660 (tt0) cc_final: 0.7316 (mt0)
REVERT: A  311 LYS cc_start: 0.8123 (mttt) cc_final: 0.7515 (tttt)
REVERT: A  317 LYS cc_start: 0.7782 (mttt) cc_final: 0.7437 (mtpt)
REVERT: A  338 GLU cc_start: 0.7557 (tt0) cc_final: 0.7256 (tm-30)
REVERT: A  369 LYS cc_start: 0.8276 (tttt) cc_final: 0.7922 (ttmm)
REVERT: F  307 GLN cc_start: 0.7894 (tt0) cc_final: 0.7458 (mt0)
REVERT: F  311 LYS cc_start: 0.8297 (mttt) cc_final: 0.7679 (pttp)
REVERT: F  342 GLU cc_start: 0.6818 (mp0) cc_final: 0.6589 (mp0)
REVERT: F  348 ASP cc_start: 0.8495 (t0) cc_final: 0.8270 (t0)
REVERT: B  317 LYS cc_start: 0.8247 (mttt) cc_final: 0.7799 (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: 0.8063 (tttp)
REVERT: C  307 GLN cc_start: 0.8202 (tt0) cc_final: 0.7915 (tt0)
REVERT: C  311 LYS cc_start: 0.8233 (mttt) cc_final: 0.7960 (mttm)
REVERT: C  317 LYS cc_start: 0.8077 (mttt) cc_final: 0.7819 (mtpp)
REVERT: C  338 GLU cc_start: 0.7874 (tt0) cc_final: 0.7642 (tt0)
REVERT: C  340 LYS cc_start: 0.7912 (tttt) cc_final: 0.7284 (mttm)
REVERT: C  369 LYS cc_start: 0.8439 (tttt) cc_final: 0.8118 (tttp)
REVERT: D  311 LYS cc_start: 0.8357 (mttt) cc_final: 0.8111 (mtmt)
REVERT: D  317 LYS cc_start: 0.7928 (mttt) cc_final: 0.7462 (mtpp)
REVERT: D  340 LYS cc_start: 0.7914 (tttt) cc_final: 0.7285 (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: 0.7175
  time to fit residues: 68.8942
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  : 0.609 
-------------------------------------------------------------------------------
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:    2.9990
   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:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   overall best weight:    2.0986

-------------------------------------------------------------------------------
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 = 0.3962 r_free = 0.3962 target = 0.130575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.116032 restraints weight = 13289.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.3788 rms_B_bonded: 1.88
r_work: 0.3719 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3638 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.4366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3498  Z= 0.201
  Angle     :  0.525   4.964   4680  Z= 0.267
  Chirality :  0.052   0.133    528
  Planarity :  0.002   0.020    594
  Dihedral  :  5.193  12.785    462
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 0.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  6.31 %
    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 : -0.75 (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 F 379 

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.586 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  369 LYS cc_start: 0.8430 (tttt) cc_final: 0.8099 (ttmm)
REVERT: A  307 GLN cc_start: 0.7726 (tt0) cc_final: 0.7370 (mt0)
REVERT: A  311 LYS cc_start: 0.8154 (mttt) cc_final: 0.7558 (tttt)
REVERT: A  317 LYS cc_start: 0.7889 (mttt) cc_final: 0.7536 (mtpt)
REVERT: A  338 GLU cc_start: 0.7633 (tt0) cc_final: 0.7358 (tm-30)
REVERT: A  347 LYS cc_start: 0.8698 (mttt) cc_final: 0.8274 (mtpp)
REVERT: A  369 LYS cc_start: 0.8245 (tttt) cc_final: 0.7928 (ttmm)
REVERT: F  307 GLN cc_start: 0.7934 (tt0) cc_final: 0.7510 (mt0)
REVERT: F  311 LYS cc_start: 0.8294 (mttt) cc_final: 0.7722 (pttt)
REVERT: F  342 GLU cc_start: 0.6953 (mp0) cc_final: 0.6705 (mp0)
REVERT: B  317 LYS cc_start: 0.8203 (mttt) cc_final: 0.7818 (mtpt)
REVERT: B  340 LYS cc_start: 0.8436 (tttt) cc_final: 0.7747 (mttm)
REVERT: B  369 LYS cc_start: 0.8428 (tttt) cc_final: 0.8101 (tttp)
REVERT: C  307 GLN cc_start: 0.8233 (tt0) cc_final: 0.7951 (tt0)
REVERT: C  317 LYS cc_start: 0.8145 (mttt) cc_final: 0.7884 (mtpp)
REVERT: C  338 GLU cc_start: 0.7792 (tt0) cc_final: 0.7519 (tt0)
REVERT: C  369 LYS cc_start: 0.8421 (tttt) cc_final: 0.8126 (tttp)
REVERT: D  311 LYS cc_start: 0.8343 (mttt) cc_final: 0.8113 (mtmt)
REVERT: D  317 LYS cc_start: 0.7920 (mttt) cc_final: 0.7511 (mtpp)
REVERT: D  351 GLN cc_start: 0.7678 (tt0) cc_final: 0.7013 (mt0)
REVERT: D  369 LYS cc_start: 0.8346 (tttt) cc_final: 0.7934 (tttp)
  outliers start: 6
  outliers final: 5
  residues processed: 79
  average time/residue: 0.7083
  time to fit residues: 61.9184
Evaluate side-chains
  72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    7.9990
   chunk 37 optimal weight:    7.9990
   chunk 10 optimal weight:    8.9990
   chunk 12 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 35 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 14 optimal weight:    6.9990
   chunk 21 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   overall best weight:    2.2984

-------------------------------------------------------------------------------
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 = 0.3967 r_free = 0.3967 target = 0.133743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.119551 restraints weight = 12850.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.3798 rms_B_bonded: 1.77
r_work: 0.3732 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3652 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.4669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3498  Z= 0.224
  Angle     :  0.508   4.892   4680  Z= 0.259
  Chirality :  0.051   0.134    528
  Planarity :  0.003   0.020    594
  Dihedral  :  5.026  13.090    462
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 1.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  :  7.07 %
    Favored  : 90.66 %
  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   0.003   0.001   HIS C 329 
 PHE   0.006   0.001   PHE B 346 
 TYR   0.009   0.002   TYR F 310 
 ARG   0.002   0.000   ARG E 379 

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  369 LYS cc_start: 0.8395 (tttt) cc_final: 0.8060 (ttmm)
REVERT: A  307 GLN cc_start: 0.7728 (tt0) cc_final: 0.7364 (mt0)
REVERT: A  315 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8636 (mt)
REVERT: A  317 LYS cc_start: 0.7918 (mttt) cc_final: 0.7540 (mtpt)
REVERT: A  338 GLU cc_start: 0.7628 (tt0) cc_final: 0.7345 (tm-30)
REVERT: A  347 LYS cc_start: 0.8660 (mttt) cc_final: 0.8356 (mtpp)
REVERT: A  369 LYS cc_start: 0.8170 (tttt) cc_final: 0.7879 (ttmm)
REVERT: F  307 GLN cc_start: 0.7912 (tt0) cc_final: 0.7484 (mt0)
REVERT: F  311 LYS cc_start: 0.8269 (mttt) cc_final: 0.7668 (pttt)
REVERT: F  341 SER cc_start: 0.8703 (m) cc_final: 0.8271 (m)
REVERT: F  342 GLU cc_start: 0.6963 (mp0) cc_final: 0.6725 (mp0)
REVERT: B  317 LYS cc_start: 0.8252 (mttt) cc_final: 0.7800 (mtpp)
REVERT: B  340 LYS cc_start: 0.8288 (tttt) cc_final: 0.7700 (mttm)
REVERT: B  369 LYS cc_start: 0.8599 (tttt) cc_final: 0.8255 (tttp)
REVERT: C  307 GLN cc_start: 0.8245 (tt0) cc_final: 0.7987 (tt0)
REVERT: C  317 LYS cc_start: 0.8237 (mttt) cc_final: 0.7962 (mtpp)
REVERT: C  338 GLU cc_start: 0.7758 (tt0) cc_final: 0.7437 (tt0)
REVERT: C  369 LYS cc_start: 0.8405 (tttt) cc_final: 0.8120 (tttp)
REVERT: D  311 LYS cc_start: 0.8286 (mttt) cc_final: 0.8060 (mtmt)
REVERT: D  317 LYS cc_start: 0.7990 (mttt) cc_final: 0.7585 (mtpp)
REVERT: D  338 GLU cc_start: 0.7885 (tt0) cc_final: 0.7676 (tt0)
REVERT: D  369 LYS cc_start: 0.8366 (tttt) cc_final: 0.7932 (tttp)
  outliers start: 9
  outliers final: 7
  residues processed: 78
  average time/residue: 0.6436
  time to fit residues: 55.8035
Evaluate side-chains
  75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
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 F residue  305 SER
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain C residue  319 THR
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:    0.9980
   chunk 21 optimal weight:    4.9990
   chunk 38 optimal weight:    8.9990
   chunk 30 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 12 optimal weight:    0.4980
   chunk 4 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 14 optimal weight:    5.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4040 r_free = 0.4040 target = 0.139259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.125677 restraints weight = 12553.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.3890 rms_B_bonded: 1.76
r_work: 0.3826 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3748 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.4885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3498  Z= 0.115
  Angle     :  0.453   4.902   4680  Z= 0.229
  Chirality :  0.051   0.142    528
  Planarity :  0.002   0.018    594
  Dihedral  :  4.496  12.182    462
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 0.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  8.08 %
    Favored  : 90.40 %
  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: -0.70 (0.40), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.53 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS C 362 
 PHE   0.002   0.000   PHE C 378 
 TYR   0.004   0.001   TYR B 310 
 ARG   0.001   0.000   ARG E 379 

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  369 LYS cc_start: 0.8393 (tttt) cc_final: 0.8080 (ttmm)
REVERT: A  307 GLN cc_start: 0.7727 (tt0) cc_final: 0.7391 (mt0)
REVERT: A  311 LYS cc_start: 0.8055 (mttt) cc_final: 0.7467 (tttt)
REVERT: A  315 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8521 (mt)
REVERT: A  338 GLU cc_start: 0.7577 (tt0) cc_final: 0.7316 (tm-30)
REVERT: A  347 LYS cc_start: 0.8682 (mttt) cc_final: 0.8380 (mtpp)
REVERT: A  369 LYS cc_start: 0.8149 (tttt) cc_final: 0.7857 (ttmm)
REVERT: A  372 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7232 (tm-30)
REVERT: F  307 GLN cc_start: 0.7919 (tt0) cc_final: 0.7492 (mt0)
REVERT: F  341 SER cc_start: 0.8683 (m) cc_final: 0.8258 (m)
REVERT: F  342 GLU cc_start: 0.6973 (mp0) cc_final: 0.6641 (mp0)
REVERT: F  369 LYS cc_start: 0.8277 (tttt) cc_final: 0.7860 (ttmm)
REVERT: B  340 LYS cc_start: 0.8303 (tttt) cc_final: 0.7766 (mttm)
REVERT: C  307 GLN cc_start: 0.8243 (tt0) cc_final: 0.7977 (tt0)
REVERT: C  311 LYS cc_start: 0.8301 (mttt) cc_final: 0.7796 (mttm)
REVERT: C  369 LYS cc_start: 0.8450 (tttt) cc_final: 0.8201 (tttp)
REVERT: D  311 LYS cc_start: 0.8292 (mttt) cc_final: 0.8059 (mtmt)
REVERT: D  317 LYS cc_start: 0.7924 (mttt) cc_final: 0.7532 (mtpp)
REVERT: D  347 LYS cc_start: 0.8675 (mmtt) cc_final: 0.8260 (mmtt)
REVERT: D  351 GLN cc_start: 0.7635 (tt0) cc_final: 0.7005 (mt0)
  outliers start: 6
  outliers final: 3
  residues processed: 76
  average time/residue: 0.6111
  time to fit residues: 52.3284
Evaluate side-chains
  65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
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  315 LEU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain B residue  311 LYS
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:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 21 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 4 optimal weight:    7.9990
   chunk 23 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   overall best weight:    1.4784

-------------------------------------------------------------------------------
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 = 0.3999 r_free = 0.3999 target = 0.135981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.122373 restraints weight = 12851.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3836 rms_B_bonded: 1.77
r_work: 0.3771 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3691 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.5042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3498  Z= 0.164
  Angle     :  0.466   4.492   4680  Z= 0.235
  Chirality :  0.051   0.132    528
  Planarity :  0.002   0.018    594
  Dihedral  :  4.493  11.416    462
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 1.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  9.09 %
    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: -0.65 (0.40), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.48 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS C 329 
 PHE   0.004   0.001   PHE F 346 
 TYR   0.007   0.002   TYR F 310 
 ARG   0.001   0.000   ARG C 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
  72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.585 
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: 0.8085 (ttmm)
REVERT: A  307 GLN cc_start: 0.7727 (tt0) cc_final: 0.7366 (mt0)
REVERT: A  311 LYS cc_start: 0.8109 (mttt) cc_final: 0.7504 (tttt)
REVERT: A  315 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8552 (mt)
REVERT: A  317 LYS cc_start: 0.7861 (mttt) cc_final: 0.7518 (mtpt)
REVERT: A  338 GLU cc_start: 0.7598 (tt0) cc_final: 0.7303 (tm-30)
REVERT: A  347 LYS cc_start: 0.8688 (mttt) cc_final: 0.8362 (mtpp)
REVERT: A  369 LYS cc_start: 0.8160 (tttt) cc_final: 0.7862 (ttmm)
REVERT: A  372 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7243 (tm-30)
REVERT: A  379 ARG cc_start: 0.5144 (tmm160) cc_final: 0.4433 (tmm-80)
REVERT: F  307 GLN cc_start: 0.7862 (tt0) cc_final: 0.7557 (mt0)
REVERT: F  342 GLU cc_start: 0.6895 (mp0) cc_final: 0.6601 (mp0)
REVERT: F  369 LYS cc_start: 0.8296 (tttt) cc_final: 0.7879 (ttmm)
REVERT: B  317 LYS cc_start: 0.8246 (mttt) cc_final: 0.7831 (mtpp)
REVERT: B  340 LYS cc_start: 0.8313 (tttt) cc_final: 0.7681 (mttm)
REVERT: B  342 GLU cc_start: 0.7371 (mp0) cc_final: 0.7131 (mp0)
REVERT: B  369 LYS cc_start: 0.8579 (tttt) cc_final: 0.8322 (tttp)
REVERT: C  307 GLN cc_start: 0.8256 (tt0) cc_final: 0.8008 (tt0)
REVERT: D  311 LYS cc_start: 0.8296 (mttt) cc_final: 0.8065 (mtmt)
REVERT: D  317 LYS cc_start: 0.7967 (mttt) cc_final: 0.7552 (mtpp)
REVERT: D  342 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6686 (mp0)
  outliers start: 6
  outliers final: 3
  residues processed: 71
  average time/residue: 0.6176
  time to fit residues: 49.1093
Evaluate side-chains
  69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 15 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 19 optimal weight:    7.9990
   chunk 38 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 29 optimal weight:    6.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
B 368 ASN
D 351 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.136327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.122838 restraints weight = 12672.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.3846 rms_B_bonded: 1.75
r_work: 0.3781 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.3702 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.5162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3498  Z= 0.149
  Angle     :  0.453   4.529   4680  Z= 0.228
  Chirality :  0.051   0.133    528
  Planarity :  0.002   0.018    594
  Dihedral  :  4.374  10.744    462
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 1.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  :  9.09 %
    Favored  : 88.89 %
  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: -0.65 (0.40), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.49 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS C 329 
 PHE   0.003   0.001   PHE B 346 
 TYR   0.006   0.001   TYR F 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
  73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.577 
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: 0.8088 (ttmm)
REVERT: E  372 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7300 (mm-30)
REVERT: A  307 GLN cc_start: 0.7732 (tt0) cc_final: 0.7381 (mt0)
REVERT: A  311 LYS cc_start: 0.8104 (mttt) cc_final: 0.7507 (tttt)
REVERT: A  315 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8541 (mt)
REVERT: A  317 LYS cc_start: 0.7851 (mttt) cc_final: 0.7524 (mtpt)
REVERT: A  338 GLU cc_start: 0.7576 (tt0) cc_final: 0.7299 (tm-30)
REVERT: A  347 LYS cc_start: 0.8680 (mttt) cc_final: 0.8358 (mtpp)
REVERT: A  369 LYS cc_start: 0.8185 (tttt) cc_final: 0.7897 (ttmm)
REVERT: A  372 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7227 (tm-30)
REVERT: A  379 ARG cc_start: 0.5298 (tmm160) cc_final: 0.4602 (tmm-80)
REVERT: F  307 GLN cc_start: 0.7865 (tt0) cc_final: 0.7566 (mt0)
REVERT: F  351 GLN cc_start: 0.7876 (tt0) cc_final: 0.7409 (mt0)
REVERT: F  369 LYS cc_start: 0.8292 (tttt) cc_final: 0.7881 (ttmm)
REVERT: B  317 LYS cc_start: 0.8229 (mttt) cc_final: 0.7867 (mtpp)
REVERT: B  340 LYS cc_start: 0.8314 (tttt) cc_final: 0.7706 (mttm)
REVERT: B  369 LYS cc_start: 0.8573 (tttt) cc_final: 0.8315 (tttp)
REVERT: C  307 GLN cc_start: 0.8258 (tt0) cc_final: 0.7999 (tt0)
REVERT: D  311 LYS cc_start: 0.8282 (mttt) cc_final: 0.8041 (mtmt)
REVERT: D  317 LYS cc_start: 0.7929 (mttt) cc_final: 0.7557 (mtpp)
REVERT: D  379 ARG cc_start: 0.7017 (mtp85) cc_final: 0.6814 (mtp85)
  outliers start: 8
  outliers final: 6
  residues processed: 72
  average time/residue: 0.6490
  time to fit residues: 52.5449
Evaluate side-chains
  70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
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 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  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:    6.9990
   chunk 15 optimal weight:    8.9990
   chunk 29 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0570
   chunk 24 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 17 optimal weight:    8.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    1.5702

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

Flipped N/Q/H residues before XYZ refinement:
B 368 ASN
D 351 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.135187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.121491 restraints weight = 12890.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3817 rms_B_bonded: 1.77
r_work: 0.3751 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3670 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.5192

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= 0.172
  Angle     :  0.473   4.831   4680  Z= 0.240
  Chirality :  0.050   0.132    528
  Planarity :  0.002   0.018    594
  Dihedral  :  4.407  11.878    462
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 1.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  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: -0.70 (0.40), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.52 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS C 329 
 PHE   0.003   0.001   PHE F 346 
 TYR   0.007   0.002   TYR A 310 
 ARG   0.001   0.000   ARG E 379 

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  351 GLN cc_start: 0.8084 (tt0) cc_final: 0.7863 (mt0)
REVERT: E  369 LYS cc_start: 0.8389 (tttt) cc_final: 0.8083 (ttmm)
REVERT: E  372 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7298 (mm-30)
REVERT: A  307 GLN cc_start: 0.7708 (tt0) cc_final: 0.7359 (mt0)
REVERT: A  311 LYS cc_start: 0.8164 (mttt) cc_final: 0.7561 (tttt)
REVERT: A  315 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8549 (mt)
REVERT: A  317 LYS cc_start: 0.7864 (mttt) cc_final: 0.7533 (mtpt)
REVERT: A  338 GLU cc_start: 0.7592 (tt0) cc_final: 0.7306 (tm-30)
REVERT: A  347 LYS cc_start: 0.8681 (mttt) cc_final: 0.8363 (mtpp)
REVERT: A  369 LYS cc_start: 0.8175 (tttt) cc_final: 0.7876 (ttmm)
REVERT: A  372 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7261 (tm-30)
REVERT: A  379 ARG cc_start: 0.5289 (tmm160) cc_final: 0.4595 (tmm-80)
REVERT: F  307 GLN cc_start: 0.7853 (tt0) cc_final: 0.7550 (mt0)
REVERT: F  311 LYS cc_start: 0.8199 (mttt) cc_final: 0.7633 (pttt)
REVERT: F  351 GLN cc_start: 0.7907 (tt0) cc_final: 0.7429 (mt0)
REVERT: F  369 LYS cc_start: 0.8307 (tttt) cc_final: 0.7887 (ttmm)
REVERT: B  317 LYS cc_start: 0.8232 (mttt) cc_final: 0.7914 (mtpp)
REVERT: B  340 LYS cc_start: 0.8331 (tttt) cc_final: 0.7784 (mttm)
REVERT: B  369 LYS cc_start: 0.8587 (tttt) cc_final: 0.8319 (tttp)
REVERT: C  307 GLN cc_start: 0.8232 (tt0) cc_final: 0.7973 (tt0)
REVERT: D  311 LYS cc_start: 0.8287 (mttt) cc_final: 0.8033 (mtmt)
REVERT: D  317 LYS cc_start: 0.7956 (mttt) cc_final: 0.7599 (mtpp)
REVERT: D  379 ARG cc_start: 0.7082 (mtp85) cc_final: 0.6822 (mtp85)
  outliers start: 9
  outliers final: 7
  residues processed: 77
  average time/residue: 0.6113
  time to fit residues: 53.1962
Evaluate side-chains
  75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
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  324 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    0.0670
   chunk 25 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 40 optimal weight:    7.9990
   chunk 29 optimal weight:    5.9990
   chunk 41 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.8126

-------------------------------------------------------------------------------
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 = 0.3978 r_free = 0.3978 target = 0.133914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.120043 restraints weight = 12799.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.3809 rms_B_bonded: 1.77
r_work: 0.3740 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3659 rms_B_bonded: 2.96 restraints_weight: 0.2500
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.5235

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= 0.189
  Angle     :  0.476   4.487   4680  Z= 0.242
  Chirality :  0.050   0.133    528
  Planarity :  0.002   0.019    594
  Dihedral  :  4.461  11.006    462
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 1.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  :  9.85 %
    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: -0.76 (0.40), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.57 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   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 C 379 

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

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  351 GLN cc_start: 0.8126 (tt0) cc_final: 0.7906 (mt0)
REVERT: E  369 LYS cc_start: 0.8392 (tttt) cc_final: 0.8080 (ttmm)
REVERT: A  307 GLN cc_start: 0.7712 (tt0) cc_final: 0.7330 (mt0)
REVERT: A  311 LYS cc_start: 0.8206 (mttt) cc_final: 0.7561 (tttt)
REVERT: A  315 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8565 (mt)
REVERT: A  317 LYS cc_start: 0.7863 (mttt) cc_final: 0.7531 (mtpt)
REVERT: A  338 GLU cc_start: 0.7616 (tt0) cc_final: 0.7306 (tm-30)
REVERT: A  347 LYS cc_start: 0.8681 (mttt) cc_final: 0.8358 (mtpp)
REVERT: A  369 LYS cc_start: 0.8176 (tttt) cc_final: 0.7880 (ttmm)
REVERT: F  307 GLN cc_start: 0.7871 (tt0) cc_final: 0.7556 (mt0)
REVERT: F  311 LYS cc_start: 0.8223 (mttt) cc_final: 0.7608 (pttt)
REVERT: F  369 LYS cc_start: 0.8342 (tttt) cc_final: 0.7910 (ttmm)
REVERT: B  317 LYS cc_start: 0.8286 (mttt) cc_final: 0.7985 (mtpp)
REVERT: B  340 LYS cc_start: 0.8350 (tttt) cc_final: 0.7758 (mttm)
REVERT: B  351 GLN cc_start: 0.7866 (tt0) cc_final: 0.7561 (mt0)
REVERT: B  369 LYS cc_start: 0.8590 (tttt) cc_final: 0.8317 (tttp)
REVERT: C  307 GLN cc_start: 0.8236 (tt0) cc_final: 0.7978 (tt0)
REVERT: D  311 LYS cc_start: 0.8266 (mttt) cc_final: 0.8021 (mtmt)
REVERT: D  317 LYS cc_start: 0.7949 (mttt) cc_final: 0.7598 (mtpp)
  outliers start: 9
  outliers final: 8
  residues processed: 73
  average time/residue: 0.6296
  time to fit residues: 51.9072
Evaluate side-chains
  73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 41 optimal weight:    7.9990
   chunk 25 optimal weight:    0.0570
   chunk 21 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 32 optimal weight:    6.9990
   chunk 18 optimal weight:    0.8980
   chunk 17 optimal weight:    7.9990
   chunk 8 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 31 optimal weight:    6.9990
   overall best weight:    2.9904

-------------------------------------------------------------------------------
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 = 0.3890 r_free = 0.3890 target = 0.121002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.105877 restraints weight = 14222.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 1.95
r_work: 0.3656 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3568 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.5237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3498  Z= 0.280
  Angle     :  0.518   4.792   4680  Z= 0.267
  Chirality :  0.050   0.133    528
  Planarity :  0.003   0.020    594
  Dihedral  :  4.744  12.050    462
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 2.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  :  9.34 %
    Favored  : 88.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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   0.003   0.001   HIS B 329 
 PHE   0.007   0.001   PHE E 378 
 TYR   0.011   0.002   TYR A 310 
 ARG   0.003   0.000   ARG D 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
  77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  347 LYS cc_start: 0.8773 (mttt) cc_final: 0.8346 (mtpp)
REVERT: E  351 GLN cc_start: 0.8281 (tt0) cc_final: 0.8030 (mt0)
REVERT: E  369 LYS cc_start: 0.8461 (tttt) cc_final: 0.8123 (ttmm)
REVERT: A  307 GLN cc_start: 0.7645 (tt0) cc_final: 0.7219 (mt0)
REVERT: A  317 LYS cc_start: 0.7846 (mttt) cc_final: 0.7489 (mtpt)
REVERT: A  338 GLU cc_start: 0.7680 (tt0) cc_final: 0.7316 (tm-30)
REVERT: A  347 LYS cc_start: 0.8677 (mttt) cc_final: 0.8336 (mtpp)
REVERT: A  369 LYS cc_start: 0.8251 (tttt) cc_final: 0.7899 (ttmm)
REVERT: F  307 GLN cc_start: 0.7874 (tt0) cc_final: 0.7465 (mt0)
REVERT: F  311 LYS cc_start: 0.8234 (mttt) cc_final: 0.7499 (pttt)
REVERT: F  369 LYS cc_start: 0.8382 (tttt) cc_final: 0.7954 (ttmm)
REVERT: B  317 LYS cc_start: 0.8391 (mttt) cc_final: 0.8094 (mtpp)
REVERT: B  340 LYS cc_start: 0.8374 (tttt) cc_final: 0.7758 (mttm)
REVERT: B  351 GLN cc_start: 0.7970 (tt0) cc_final: 0.7466 (mt0)
REVERT: B  369 LYS cc_start: 0.8665 (tttt) cc_final: 0.8384 (tttp)
REVERT: C  307 GLN cc_start: 0.8199 (tt0) cc_final: 0.7935 (tt0)
REVERT: C  311 LYS cc_start: 0.8433 (mttt) cc_final: 0.7711 (tttt)
REVERT: D  311 LYS cc_start: 0.8355 (mttt) cc_final: 0.8080 (mtmt)
REVERT: D  317 LYS cc_start: 0.8007 (mttt) cc_final: 0.7652 (mtpp)
REVERT: D  369 LYS cc_start: 0.8443 (tttt) cc_final: 0.7987 (tttp)
  outliers start: 10
  outliers final: 9
  residues processed: 76
  average time/residue: 0.6544
  time to fit residues: 55.5887
Evaluate side-chains
  74 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
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  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
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:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 6 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 4 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    1.9388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.122316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.107437 restraints weight = 13977.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 1.93
r_work: 0.3659 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3572 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.5285

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= 0.198
  Angle     :  0.490   4.901   4680  Z= 0.251
  Chirality :  0.051   0.134    528
  Planarity :  0.003   0.019    594
  Dihedral  :  4.607  11.268    462
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 1.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  :  9.85 %
    Favored  : 88.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.39), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.75 (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 E 378 
 TYR   0.007   0.002   TYR A 310 
 ARG   0.001   0.000   ARG A 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4599.15 seconds
wall clock time: 81 minutes 41.33 seconds (4901.33 seconds total)