Starting phenix.real_space_refine
on Wed Feb 12 03:09:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q8d_18251/02_2025/8q8d_18251.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q8d_18251/02_2025/8q8d_18251.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q8d_18251/02_2025/8q8d_18251.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q8d_18251/02_2025/8q8d_18251.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q8d_18251/02_2025/8q8d_18251.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q8d_18251/02_2025/8q8d_18251.cif"
  }
  resolution = 3.04
  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    2172      2.51       5
     N     642      2.21       5
     O     648      1.98       5
     H    3606      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 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: 7074
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 1179
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "B"
      Number of atoms: 1179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 1179
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "C"
      Number of atoms: 1179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 1179
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "D"
      Number of atoms: 1179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 1179
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "E"
      Number of atoms: 1179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 1179
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "F"
      Number of atoms: 1179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 1179
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
  Time building chain proxies: 5.16, per 1000 atoms: 0.73
  Number of scatterers: 7074
  At special positions: 0
  Unit cell: (119.48, 117.832, 39.552, 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     648      8.00
     N     642      7.00
     C    2172      6.00
     H    3606      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: 1.70
  Conformation dependent library (CDL) restraints added in 658.5 milliseconds
  

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 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 19 sheets defined
      0.0% alpha, 48.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310
      removed outlier: 6.519A  pdb=" N   GLN A 307 " --> pdb=" O   ILE C 308 " (cutoff:3.500A)
      removed outlier: 7.751A  pdb=" N   TYR C 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   VAL A 309 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   VAL A 306 " --> pdb=" O   GLN E 307 " (cutoff:3.500A)
      removed outlier: 7.712A  pdb=" N   VAL E 309 " --> pdb=" O   VAL A 306 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   ILE A 308 " --> pdb=" O   VAL E 309 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314
      removed outlier: 6.852A  pdb=" N   VAL A 313 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 318
      removed outlier: 6.441A  pdb=" N   LYS A 317 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 321 through 322
      removed outlier: 6.385A  pdb=" N   LYS A 321 " --> pdb=" O   CYS C 322 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 328 through 330
      removed outlier: 6.375A  pdb=" N   ILE A 328 " --> pdb=" O   HIS E 329 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 336 through 340
      removed outlier: 6.626A  pdb=" N   VAL A 337 " --> pdb=" O   GLU E 338 " (cutoff:3.500A)
      removed outlier: 7.882A  pdb=" N   LYS E 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   VAL A 339 " --> pdb=" O   LYS E 340 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 343 through 346
      removed outlier: 6.267A  pdb=" N   LYS A 343 " --> pdb=" O   LEU C 344 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   PHE C 346 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   ASP A 345 " --> pdb=" O   PHE C 346 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 351 through 354
      removed outlier: 6.409A  pdb=" N   GLN A 351 " --> pdb=" O   SER C 352 " (cutoff:3.500A)
      removed outlier: 7.760A  pdb=" N   ILE C 354 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   LYS A 353 " --> pdb=" O   ILE C 354 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 357 through 362
      removed outlier: 6.460A  pdb=" N   ASP A 358 " --> pdb=" O   ASN C 359 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   THR C 361 " --> pdb=" O   ASP A 358 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ILE A 360 " --> pdb=" O   THR C 361 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 369 through 378
      removed outlier: 6.380A  pdb=" N   LYS A 369 " --> pdb=" O   LYS C 370 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   GLU C 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   ILE A 371 " --> pdb=" O   GLU C 372 " (cutoff:3.500A)
      removed outlier: 7.976A  pdb=" N   HIS C 374 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 6.084A  pdb=" N   THR A 373 " --> pdb=" O   HIS C 374 " (cutoff:3.500A)
      removed outlier: 8.011A  pdb=" N   LEU C 376 " --> pdb=" O   THR A 373 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   LYS A 375 " --> pdb=" O   LEU C 376 " (cutoff:3.500A)
      removed outlier: 7.901A  pdb=" N   PHE C 378 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   THR A 377 " --> pdb=" O   PHE C 378 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   LYS A 370 " --> pdb=" O   ILE E 371 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   THR E 373 " --> pdb=" O   LYS A 370 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   GLU A 372 " --> pdb=" O   THR E 373 " (cutoff:3.500A)
      removed outlier: 8.384A  pdb=" N   LYS E 375 " --> pdb=" O   GLU A 372 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   HIS A 374 " --> pdb=" O   LYS E 375 " (cutoff:3.500A)
      removed outlier: 7.994A  pdb=" N   THR E 377 " --> pdb=" O   HIS A 374 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   LEU A 376 " --> pdb=" O   THR E 377 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'D' and resid 306 through 310
      removed outlier: 6.491A  pdb=" N   GLN B 307 " --> pdb=" O   ILE D 308 " (cutoff:3.500A)
      removed outlier: 7.643A  pdb=" N   TYR D 310 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   VAL B 309 " --> pdb=" O   TYR D 310 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 313 through 314
      removed outlier: 6.800A  pdb=" N   VAL B 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 317 through 325
      removed outlier: 6.243A  pdb=" N   LYS B 317 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
      removed outlier: 8.061A  pdb=" N   SER D 320 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   THR B 319 " --> pdb=" O   SER D 320 " (cutoff:3.500A)
      removed outlier: 7.997A  pdb=" N   CYS D 322 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   LYS B 321 " --> pdb=" O   CYS D 322 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   SER D 324 " --> pdb=" O   LYS B 321 " (cutoff:3.500A)
      removed outlier: 6.120A  pdb=" N   GLY B 323 " --> pdb=" O   SER D 324 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 328 through 330
    Processing sheet with id=AB6, first strand: chain 'D' and resid 336 through 342
      removed outlier: 6.389A  pdb=" N   VAL B 337 " --> pdb=" O   GLU F 338 " (cutoff:3.500A)
      removed outlier: 7.885A  pdb=" N   LYS F 340 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   VAL B 339 " --> pdb=" O   LYS F 340 " (cutoff:3.500A)
      removed outlier: 8.052A  pdb=" N   GLU F 342 " --> pdb=" O   VAL B 339 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   SER B 341 " --> pdb=" O   GLU F 342 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 345 through 346
      removed outlier: 6.817A  pdb=" N   ASP B 345 " --> pdb=" O   PHE D 346 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 350 through 354
      removed outlier: 6.730A  pdb=" N   GLN B 351 " --> pdb=" O   SER D 352 " (cutoff:3.500A)
      removed outlier: 8.207A  pdb=" N   ILE D 354 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   LYS B 353 " --> pdb=" O   ILE D 354 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 357 through 362
      removed outlier: 6.514A  pdb=" N   ASP B 358 " --> pdb=" O   ASN D 359 " (cutoff:3.500A)
      removed outlier: 7.942A  pdb=" N   THR D 361 " --> pdb=" O   ASP B 358 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ILE B 360 " --> pdb=" O   THR D 361 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 368 through 378
      removed outlier: 6.424A  pdb=" N   LYS B 369 " --> pdb=" O   LYS D 370 " (cutoff:3.500A)
      removed outlier: 7.949A  pdb=" N   GLU D 372 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   ILE B 371 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
      removed outlier: 7.946A  pdb=" N   HIS D 374 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   THR B 373 " --> pdb=" O   HIS D 374 " (cutoff:3.500A)
      removed outlier: 7.628A  pdb=" N   LEU D 376 " --> pdb=" O   THR B 373 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   LYS B 375 " --> pdb=" O   LEU D 376 " (cutoff:3.500A)
      removed outlier: 7.882A  pdb=" N   PHE D 378 " --> pdb=" O   LYS B 375 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   THR B 377 " --> pdb=" O   PHE D 378 " (cutoff:3.500A)

    63 hydrogen bonds defined for protein.
    189 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: 2.35

  Time building geometry restraints manager: 2.02 seconds

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

  Histogram of bond lengths:
        0.94 -     1.12: 3600
        1.12 -     1.29: 579
        1.29 -     1.47: 1174
        1.47 -     1.64: 1769
        1.64 -     1.82: 6
  Bond restraints: 7128
  Sorted by residual:
  bond pdb=" N   THR E 377 "
       pdb=" H   THR E 377 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.72e+01
  bond pdb=" N   GLU A 342 "
       pdb=" H   GLU A 342 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" N   ILE C 371 "
       pdb=" H   ILE C 371 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" N   GLU E 342 "
       pdb=" H   GLU E 342 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" CZ  PHE E 378 "
       pdb=" HZ  PHE E 378 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.70e+01
  ... (remaining 7123 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.51: 10932
        2.51 -     5.02: 1556
        5.02 -     7.53: 466
        7.53 -    10.04: 21
       10.04 -    12.55: 9
  Bond angle restraints: 12984
  Sorted by residual:
  angle pdb=" CA  ASP D 358 "
        pdb=" CB  ASP D 358 "
        pdb=" CG  ASP D 358 "
      ideal   model   delta    sigma   weight residual
     112.60  118.99   -6.39 1.00e+00 1.00e+00 4.08e+01
  angle pdb=" CA  ASP B 358 "
        pdb=" CB  ASP B 358 "
        pdb=" CG  ASP B 358 "
      ideal   model   delta    sigma   weight residual
     112.60  118.59   -5.99 1.00e+00 1.00e+00 3.59e+01
  angle pdb=" C   LYS C 331 "
        pdb=" CA  LYS C 331 "
        pdb=" CB  LYS C 331 "
      ideal   model   delta    sigma   weight residual
     110.55  120.21   -9.66 1.66e+00 3.63e-01 3.39e+01
  angle pdb=" N   SER C 324 "
        pdb=" CA  SER C 324 "
        pdb=" CB  SER C 324 "
      ideal   model   delta    sigma   weight residual
     111.24  102.10    9.14 1.58e+00 4.01e-01 3.35e+01
  angle pdb=" CA  PHE E 346 "
        pdb=" CB  PHE E 346 "
        pdb=" CG  PHE E 346 "
      ideal   model   delta    sigma   weight residual
     113.80  119.34   -5.54 1.00e+00 1.00e+00 3.07e+01
  ... (remaining 12979 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 2940
       17.99 -    35.98: 158
       35.98 -    53.98: 83
       53.98 -    71.97: 96
       71.97 -    89.96: 5
  Dihedral angle restraints: 3282
    sinusoidal: 1878
      harmonic: 1404
  Sorted by residual:
  dihedral pdb=" CA  GLY C 323 "
           pdb=" C   GLY C 323 "
           pdb=" N   SER C 324 "
           pdb=" CA  SER C 324 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.83   29.17     0      5.00e+00 4.00e-02 3.40e+01
  dihedral pdb=" CA  SER A 341 "
           pdb=" C   SER A 341 "
           pdb=" N   GLU A 342 "
           pdb=" CA  GLU A 342 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.25   28.75     0      5.00e+00 4.00e-02 3.31e+01
  dihedral pdb=" CA  SER C 341 "
           pdb=" C   SER C 341 "
           pdb=" N   GLU C 342 "
           pdb=" CA  GLU C 342 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.64   28.36     0      5.00e+00 4.00e-02 3.22e+01
  ... (remaining 3279 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 323
       0.073 -    0.145: 165
       0.145 -    0.218: 34
       0.218 -    0.290: 4
       0.290 -    0.363: 2
  Chirality restraints: 528
  Sorted by residual:
  chirality pdb=" CA  CYS F 322 "
            pdb=" N   CYS F 322 "
            pdb=" C   CYS F 322 "
            pdb=" CB  CYS F 322 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.29e+00
  chirality pdb=" CA  SER C 324 "
            pdb=" N   SER C 324 "
            pdb=" C   SER C 324 "
            pdb=" CB  SER C 324 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.81   -0.30 2.00e-01 2.50e+01 2.24e+00
  chirality pdb=" CA  LYS E 347 "
            pdb=" N   LYS E 347 "
            pdb=" C   LYS E 347 "
            pdb=" CB  LYS E 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.09e+00
  ... (remaining 525 not shown)

  Planarity restraints: 1032
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 310 "    0.178 2.00e-02 2.50e+03   7.97e-02 1.91e+02
        pdb=" CG  TYR E 310 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 310 "   -0.053 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 310 "   -0.051 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 310 "   -0.056 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 310 "   -0.035 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 310 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR E 310 "    0.172 2.00e-02 2.50e+03
        pdb=" HD1 TYR E 310 "   -0.021 2.00e-02 2.50e+03
        pdb=" HD2 TYR E 310 "   -0.049 2.00e-02 2.50e+03
        pdb=" HE1 TYR E 310 "   -0.036 2.00e-02 2.50e+03
        pdb=" HE2 TYR E 310 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 310 "    0.127 2.00e-02 2.50e+03   5.36e-02 8.63e+01
        pdb=" CG  TYR A 310 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 310 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 310 "   -0.037 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 310 "   -0.034 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 310 "   -0.019 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 310 "    0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR A 310 "    0.105 2.00e-02 2.50e+03
        pdb=" HD1 TYR A 310 "   -0.016 2.00e-02 2.50e+03
        pdb=" HD2 TYR A 310 "   -0.041 2.00e-02 2.50e+03
        pdb=" HE1 TYR A 310 "   -0.023 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  TYR B 310 "   -0.083 2.00e-02 2.50e+03   3.78e-02 4.28e+01
        pdb=" CG  TYR B 310 "    0.012 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 310 "    0.025 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 310 "    0.027 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 310 "    0.029 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 310 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 310 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 310 "   -0.078 2.00e-02 2.50e+03
        pdb=" HD1 TYR B 310 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD2 TYR B 310 "    0.030 2.00e-02 2.50e+03
        pdb=" HE1 TYR B 310 "    0.025 2.00e-02 2.50e+03
        pdb=" HE2 TYR B 310 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1029 not shown)

  Histogram of nonbonded interaction distances:
        1.54 -     2.16: 504
        2.16 -     2.77: 11738
        2.77 -     3.38: 18515
        3.38 -     3.99: 25771
        3.99 -     4.60: 35517
  Nonbonded interactions: 92045
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C 314 "
            pdb=" HG  SER C 316 "
     model   vdw
     1.545 2.450
  nonbonded pdb=" OD1 ASP A 314 "
            pdb=" HG  SER A 316 "
     model   vdw
     1.545 2.450
  nonbonded pdb=" OD1 ASP F 314 "
            pdb=" HG  SER F 316 "
     model   vdw
     1.548 2.450
  nonbonded pdb=" OD1 ASP B 314 "
            pdb=" HG  SER B 316 "
     model   vdw
     1.556 2.450
  nonbonded pdb=" OD1 ASP D 314 "
            pdb=" HG  SER D 316 "
     model   vdw
     1.585 2.450
  ... (remaining 92040 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:             8.810
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     20.550
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7270
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   0.064   3522  Z= 0.745
  Angle     :  1.850  10.333   4710  Z= 1.226
  Chirality :  0.085   0.363    528
  Planarity :  0.011   0.093    600
  Dihedral  : 13.263  89.960   1350
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Cbeta Deviations :  0.51 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.32), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.25 (0.24), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.003   HIS A 330 
 PHE   0.033   0.010   PHE F 346 
 TYR   0.161   0.038   TYR E 310 
 ARG   0.003   0.001   ARG E 349 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 LYS cc_start: 0.6939 (mttt) cc_final: 0.6655 (mtpt)
REVERT: A  348 ASP cc_start: 0.7612 (t0) cc_final: 0.7404 (t70)
REVERT: A  351 GLN cc_start: 0.7228 (mt0) cc_final: 0.6743 (mp10)
REVERT: A  369 LYS cc_start: 0.7297 (mtmt) cc_final: 0.6864 (mttp)
REVERT: B  307 GLN cc_start: 0.7224 (tt0) cc_final: 0.6683 (mt0)
REVERT: B  321 LYS cc_start: 0.7258 (mttt) cc_final: 0.7020 (mttp)
REVERT: B  336 GLN cc_start: 0.7944 (mt0) cc_final: 0.7739 (mt0)
REVERT: B  338 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6598 (tp30)
REVERT: B  369 LYS cc_start: 0.7696 (tttt) cc_final: 0.7074 (ttmm)
REVERT: B  375 LYS cc_start: 0.6979 (ttmt) cc_final: 0.6374 (tttm)
REVERT: C  317 LYS cc_start: 0.7787 (mttt) cc_final: 0.7431 (mtpt)
REVERT: C  340 LYS cc_start: 0.8536 (mttt) cc_final: 0.8290 (mmmm)
REVERT: C  351 GLN cc_start: 0.7709 (mt0) cc_final: 0.7392 (mp10)
REVERT: C  375 LYS cc_start: 0.7984 (ttmt) cc_final: 0.7699 (ttmt)
REVERT: D  307 GLN cc_start: 0.7800 (tt0) cc_final: 0.7332 (mt0)
REVERT: D  347 LYS cc_start: 0.8391 (mptt) cc_final: 0.6751 (mtmm)
REVERT: D  357 LEU cc_start: 0.7731 (tp) cc_final: 0.7526 (mp)
REVERT: D  369 LYS cc_start: 0.8370 (tttt) cc_final: 0.7654 (ttmm)
REVERT: D  375 LYS cc_start: 0.8365 (ttmt) cc_final: 0.7853 (tttp)
REVERT: E  343 LYS cc_start: 0.7281 (mtmt) cc_final: 0.7012 (mtpp)
REVERT: E  351 GLN cc_start: 0.7114 (mt0) cc_final: 0.6728 (mp10)
REVERT: E  369 LYS cc_start: 0.7479 (mtmt) cc_final: 0.6987 (mttp)
REVERT: F  307 GLN cc_start: 0.7055 (tt0) cc_final: 0.6524 (mt0)
REVERT: F  311 LYS cc_start: 0.7808 (mttt) cc_final: 0.6518 (tppt)
REVERT: F  336 GLN cc_start: 0.7699 (mt0) cc_final: 0.7390 (mt0)
REVERT: F  340 LYS cc_start: 0.7593 (ttpp) cc_final: 0.6789 (mmtt)
REVERT: F  358 ASP cc_start: 0.7695 (m-30) cc_final: 0.7339 (m-30)
REVERT: F  375 LYS cc_start: 0.7523 (ttmt) cc_final: 0.7080 (tttm)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.5965
  time to fit residues: 88.4694
Evaluate side-chains
  90 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
E 362 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.137585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.125620 restraints weight = 13761.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3913 rms_B_bonded: 1.69
r_work: 0.3849 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3774 rms_B_bonded: 3.01 restraints_weight: 0.2500
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.3505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3522  Z= 0.297
  Angle     :  0.613   4.222   4710  Z= 0.325
  Chirality :  0.052   0.149    528
  Planarity :  0.004   0.052    600
  Dihedral  :  6.566  23.115    468
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 1.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  8.33 %
    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: -1.55 (0.32), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.18 (0.24), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 330 
 PHE   0.007   0.001   PHE E 346 
 TYR   0.014   0.002   TYR A 310 
 ARG   0.002   0.001   ARG F 349 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  314 ASP cc_start: 0.8141 (t0) cc_final: 0.7711 (t0)
REVERT: A  351 GLN cc_start: 0.7824 (mt0) cc_final: 0.7583 (mp10)
REVERT: A  369 LYS cc_start: 0.8274 (mtmt) cc_final: 0.8031 (mttp)
REVERT: A  372 GLU cc_start: 0.8122 (tt0) cc_final: 0.7912 (tt0)
REVERT: B  307 GLN cc_start: 0.7721 (tt0) cc_final: 0.7513 (mt0)
REVERT: B  340 LYS cc_start: 0.7790 (mtpp) cc_final: 0.6923 (mtmm)
REVERT: B  369 LYS cc_start: 0.8588 (tttt) cc_final: 0.8205 (ttmm)
REVERT: B  375 LYS cc_start: 0.8188 (ttmt) cc_final: 0.7761 (tttm)
REVERT: D  307 GLN cc_start: 0.8004 (tt0) cc_final: 0.7727 (mt0)
REVERT: D  347 LYS cc_start: 0.8413 (mptt) cc_final: 0.6840 (mtmt)
REVERT: D  375 LYS cc_start: 0.8521 (ttmt) cc_final: 0.8312 (tttp)
REVERT: E  351 GLN cc_start: 0.7818 (mt0) cc_final: 0.7593 (mp10)
REVERT: E  372 GLU cc_start: 0.8422 (tt0) cc_final: 0.8115 (tt0)
REVERT: F  307 GLN cc_start: 0.7858 (tt0) cc_final: 0.7504 (mt0)
REVERT: F  311 LYS cc_start: 0.8437 (mttt) cc_final: 0.7444 (tppt)
REVERT: F  338 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7634 (tp30)
REVERT: F  340 LYS cc_start: 0.7837 (ttpp) cc_final: 0.7100 (mmtt)
REVERT: F  375 LYS cc_start: 0.8517 (ttmt) cc_final: 0.8312 (tttm)
  outliers start: 4
  outliers final: 4
  residues processed: 101
  average time/residue: 0.6529
  time to fit residues: 72.9986
Evaluate side-chains
  88 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 84
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  345 ASP
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain F residue  341 SER
Chi-restraints excluded: chain F residue  345 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 39 optimal weight:    0.6980
   chunk 9 optimal weight:    5.9990
   chunk 34 optimal weight:    0.0270
   chunk 0 optimal weight:    2.9990
   overall best weight:    2.3444

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.134717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.123267 restraints weight = 14086.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3870 rms_B_bonded: 1.66
r_work: 0.3805 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3734 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.4651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3522  Z= 0.246
  Angle     :  0.525   4.076   4710  Z= 0.276
  Chirality :  0.052   0.132    528
  Planarity :  0.003   0.026    600
  Dihedral  :  5.809  22.702    468
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 0.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  9.60 %
    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: -1.30 (0.33), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.98 (0.25), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 330 
 PHE   0.005   0.001   PHE F 346 
 TYR   0.011   0.002   TYR C 310 
 ARG   0.006   0.001   ARG A 349 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
REVERT: A  314 ASP cc_start: 0.8232 (t0) cc_final: 0.7734 (t0)
REVERT: A  348 ASP cc_start: 0.8100 (t0) cc_final: 0.7872 (t70)
REVERT: A  349 ARG cc_start: 0.7860 (mtm180) cc_final: 0.7612 (mtm180)
REVERT: A  351 GLN cc_start: 0.7820 (mt0) cc_final: 0.7555 (mp10)
REVERT: B  307 GLN cc_start: 0.7922 (tt0) cc_final: 0.7626 (mt0)
REVERT: B  340 LYS cc_start: 0.7821 (mtpp) cc_final: 0.6987 (mtmm)
REVERT: B  369 LYS cc_start: 0.8631 (tttt) cc_final: 0.8249 (ttmm)
REVERT: B  375 LYS cc_start: 0.8305 (ttmt) cc_final: 0.7953 (tttp)
REVERT: D  307 GLN cc_start: 0.8174 (tt0) cc_final: 0.7841 (mt0)
REVERT: D  336 GLN cc_start: 0.8423 (mt0) cc_final: 0.8215 (tt0)
REVERT: D  375 LYS cc_start: 0.8597 (ttmt) cc_final: 0.8378 (tttp)
REVERT: E  351 GLN cc_start: 0.7856 (mt0) cc_final: 0.7598 (mp10)
REVERT: F  307 GLN cc_start: 0.7867 (tt0) cc_final: 0.7569 (mt0)
REVERT: F  311 LYS cc_start: 0.8490 (mttt) cc_final: 0.7459 (tppt)
REVERT: F  340 LYS cc_start: 0.7663 (ttpp) cc_final: 0.7116 (mmtt)
REVERT: F  375 LYS cc_start: 0.8573 (ttmt) cc_final: 0.8357 (tttm)
  outliers start: 6
  outliers final: 5
  residues processed: 88
  average time/residue: 0.6234
  time to fit residues: 61.6053
Evaluate side-chains
  80 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain F residue  341 SER
Chi-restraints excluded: chain F residue  345 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 24 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 21 optimal weight:    0.6980
   chunk 11 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 40 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0770
   chunk 28 optimal weight:    3.9990
   overall best weight:    1.7142

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.134151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.122570 restraints weight = 14080.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3863 rms_B_bonded: 1.76
r_work: 0.3791 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.3716 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.5122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3522  Z= 0.192
  Angle     :  0.482   3.997   4710  Z= 0.251
  Chirality :  0.051   0.134    528
  Planarity :  0.004   0.042    600
  Dihedral  :  5.353  21.484    468
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 1.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  9.85 %
    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: -1.21 (0.34), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.92 (0.26), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B 374 
 PHE   0.003   0.001   PHE B 378 
 TYR   0.010   0.002   TYR C 310 
 ARG   0.004   0.000   ARG B 379 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.585 
Fit side-chains
REVERT: A  314 ASP cc_start: 0.8235 (t0) cc_final: 0.7862 (t0)
REVERT: A  351 GLN cc_start: 0.7865 (mt0) cc_final: 0.7580 (mp10)
REVERT: A  372 GLU cc_start: 0.8400 (tt0) cc_final: 0.8144 (tt0)
REVERT: B  307 GLN cc_start: 0.8038 (tt0) cc_final: 0.7596 (mt0)
REVERT: B  340 LYS cc_start: 0.7813 (mtpp) cc_final: 0.6987 (mtmm)
REVERT: B  369 LYS cc_start: 0.8632 (tttt) cc_final: 0.8208 (ttmm)
REVERT: B  375 LYS cc_start: 0.8335 (ttmt) cc_final: 0.7970 (tttp)
REVERT: D  307 GLN cc_start: 0.8237 (tt0) cc_final: 0.7798 (mt0)
REVERT: D  336 GLN cc_start: 0.8448 (mt0) cc_final: 0.8231 (tt0)
REVERT: D  375 LYS cc_start: 0.8650 (ttmt) cc_final: 0.8387 (tttp)
REVERT: E  340 LYS cc_start: 0.8646 (mtmt) cc_final: 0.8415 (mtmt)
REVERT: E  343 LYS cc_start: 0.7771 (mtpp) cc_final: 0.7264 (ttpt)
REVERT: E  351 GLN cc_start: 0.7895 (mt0) cc_final: 0.7559 (mp10)
REVERT: F  307 GLN cc_start: 0.7928 (tt0) cc_final: 0.7562 (mt0)
REVERT: F  311 LYS cc_start: 0.8489 (mttt) cc_final: 0.7442 (tppt)
REVERT: F  340 LYS cc_start: 0.7715 (ttpp) cc_final: 0.7078 (mmtt)
REVERT: F  347 LYS cc_start: 0.8070 (mmtm) cc_final: 0.7866 (mmtm)
REVERT: F  375 LYS cc_start: 0.8576 (ttmt) cc_final: 0.8327 (tttm)
  outliers start: 7
  outliers final: 7
  residues processed: 83
  average time/residue: 0.5558
  time to fit residues: 52.1205
Evaluate side-chains
  77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  345 ASP
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain F residue  341 SER
Chi-restraints excluded: chain F residue  345 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 13 optimal weight:    7.9990
   chunk 30 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 3 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.128875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.117332 restraints weight = 14182.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3791 rms_B_bonded: 1.74
r_work: 0.3718 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.3641 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.5443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   3522  Z= 0.339
  Angle     :  0.516   4.072   4710  Z= 0.273
  Chirality :  0.050   0.128    528
  Planarity :  0.003   0.024    600
  Dihedral  :  5.477  22.067    468
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 0.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 11.87 %
    Favored  : 86.36 %
  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: -1.22 (0.35), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.92 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 362 
 PHE   0.004   0.001   PHE C 378 
 TYR   0.006   0.001   TYR A 310 
 ARG   0.002   0.001   ARG F 349 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 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: 7
    poor density    : 71
  time to evaluate  : 0.569 
Fit side-chains
REVERT: A  314 ASP cc_start: 0.8231 (t0) cc_final: 0.7789 (t0)
REVERT: A  372 GLU cc_start: 0.8428 (tt0) cc_final: 0.8125 (tt0)
REVERT: B  340 LYS cc_start: 0.7927 (mtpp) cc_final: 0.7062 (mtmm)
REVERT: B  369 LYS cc_start: 0.8694 (tttt) cc_final: 0.8238 (ttmm)
REVERT: B  375 LYS cc_start: 0.8406 (ttmt) cc_final: 0.8057 (tttp)
REVERT: D  307 GLN cc_start: 0.8423 (tt0) cc_final: 0.7894 (mt0)
REVERT: D  336 GLN cc_start: 0.8530 (mt0) cc_final: 0.8290 (tt0)
REVERT: D  369 LYS cc_start: 0.8678 (tttt) cc_final: 0.8205 (ttmm)
REVERT: D  375 LYS cc_start: 0.8717 (ttmt) cc_final: 0.8456 (tttp)
REVERT: E  340 LYS cc_start: 0.8713 (mtmt) cc_final: 0.8481 (mtmt)
REVERT: E  343 LYS cc_start: 0.7931 (mtpp) cc_final: 0.7436 (ttpp)
REVERT: F  307 GLN cc_start: 0.8072 (tt0) cc_final: 0.7599 (mt0)
REVERT: F  324 SER cc_start: 0.8861 (m) cc_final: 0.8643 (t)
REVERT: F  340 LYS cc_start: 0.7731 (ttpp) cc_final: 0.7102 (mmtt)
REVERT: F  347 LYS cc_start: 0.8129 (mmtm) cc_final: 0.7924 (mmtm)
REVERT: F  375 LYS cc_start: 0.8605 (ttmt) cc_final: 0.8353 (tttm)
  outliers start: 7
  outliers final: 7
  residues processed: 77
  average time/residue: 0.6174
  time to fit residues: 53.5506
Evaluate side-chains
  71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain F residue  341 SER
Chi-restraints excluded: chain F residue  345 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   chunk 36 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   chunk 7 optimal weight:    5.9990
   chunk 20 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.131025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.119591 restraints weight = 14033.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.3825 rms_B_bonded: 1.74
r_work: 0.3750 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.3675 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.5602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3522  Z= 0.183
  Angle     :  0.470   3.960   4710  Z= 0.245
  Chirality :  0.051   0.130    528
  Planarity :  0.003   0.032    600
  Dihedral  :  5.218  20.886    468
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 1.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 11.87 %
    Favored  : 85.86 %
  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: -1.26 (0.35), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.95 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C 330 
 PHE   0.002   0.001   PHE B 346 
 TYR   0.006   0.001   TYR C 310 
 ARG   0.005   0.000   ARG B 379 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.603 
Fit side-chains
REVERT: A  314 ASP cc_start: 0.8226 (t0) cc_final: 0.7768 (t0)
REVERT: A  372 GLU cc_start: 0.8425 (tt0) cc_final: 0.8127 (tt0)
REVERT: B  340 LYS cc_start: 0.7821 (mtpp) cc_final: 0.6974 (mtmm)
REVERT: B  369 LYS cc_start: 0.8692 (tttt) cc_final: 0.8226 (ttmm)
REVERT: B  375 LYS cc_start: 0.8338 (ttmt) cc_final: 0.8016 (tttp)
REVERT: D  307 GLN cc_start: 0.8387 (tt0) cc_final: 0.7849 (mt0)
REVERT: D  336 GLN cc_start: 0.8502 (mt0) cc_final: 0.8254 (tt0)
REVERT: D  375 LYS cc_start: 0.8691 (ttmt) cc_final: 0.8431 (tttp)
REVERT: E  340 LYS cc_start: 0.8721 (mtmt) cc_final: 0.8498 (mtmt)
REVERT: E  343 LYS cc_start: 0.7926 (mtpp) cc_final: 0.7493 (ttpp)
REVERT: F  307 GLN cc_start: 0.8041 (tt0) cc_final: 0.7568 (mt0)
REVERT: F  324 SER cc_start: 0.8801 (m) cc_final: 0.8596 (t)
REVERT: F  340 LYS cc_start: 0.7718 (ttpp) cc_final: 0.7075 (mmtt)
REVERT: F  347 LYS cc_start: 0.8143 (mmtm) cc_final: 0.7935 (mmtm)
REVERT: F  375 LYS cc_start: 0.8632 (ttmt) cc_final: 0.8382 (tttm)
  outliers start: 9
  outliers final: 8
  residues processed: 79
  average time/residue: 0.5903
  time to fit residues: 52.8334
Evaluate side-chains
  77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  345 ASP
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain F residue  341 SER
Chi-restraints excluded: chain F residue  345 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 4 optimal weight:    8.9990
   chunk 27 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0770
   chunk 22 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0970
   chunk 13 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 2 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.135155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.124257 restraints weight = 13659.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.3888 rms_B_bonded: 1.68
r_work: 0.3818 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.3747 rms_B_bonded: 3.04 restraints_weight: 0.2500
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.5757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3522  Z= 0.118
  Angle     :  0.437   3.908   4710  Z= 0.224
  Chirality :  0.052   0.130    528
  Planarity :  0.003   0.031    600
  Dihedral  :  4.731  19.542    468
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 0.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 12.88 %
    Favored  : 86.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.36), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.92 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.000   HIS C 362 
 PHE   0.002   0.000   PHE E 346 
 TYR   0.007   0.001   TYR C 310 
 ARG   0.004   0.001   ARG B 379 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 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: 4
    poor density    : 70
  time to evaluate  : 0.613 
Fit side-chains
REVERT: A  314 ASP cc_start: 0.8200 (t0) cc_final: 0.7675 (t0)
REVERT: A  372 GLU cc_start: 0.8410 (tt0) cc_final: 0.8186 (tt0)
REVERT: B  340 LYS cc_start: 0.7738 (mtpp) cc_final: 0.6819 (mttm)
REVERT: B  369 LYS cc_start: 0.8680 (tttt) cc_final: 0.8204 (ttmm)
REVERT: B  375 LYS cc_start: 0.8346 (ttmt) cc_final: 0.8045 (tttm)
REVERT: C  348 ASP cc_start: 0.7418 (p0) cc_final: 0.6777 (p0)
REVERT: D  307 GLN cc_start: 0.8260 (tt0) cc_final: 0.7761 (mt0)
REVERT: D  336 GLN cc_start: 0.8439 (mt0) cc_final: 0.8184 (tt0)
REVERT: D  375 LYS cc_start: 0.8639 (ttmt) cc_final: 0.8388 (tttp)
REVERT: E  343 LYS cc_start: 0.7914 (mtpp) cc_final: 0.7544 (ttpp)
REVERT: F  307 GLN cc_start: 0.7996 (tt0) cc_final: 0.7521 (mt0)
REVERT: F  340 LYS cc_start: 0.7725 (ttpp) cc_final: 0.7084 (mmtt)
REVERT: F  347 LYS cc_start: 0.8180 (mmtm) cc_final: 0.7969 (mmtm)
REVERT: F  375 LYS cc_start: 0.8613 (ttmt) cc_final: 0.8364 (tttm)
  outliers start: 4
  outliers final: 4
  residues processed: 73
  average time/residue: 0.6049
  time to fit residues: 50.6974
Evaluate side-chains
  69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain E residue  325 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 33 optimal weight:    5.9990
   chunk 4 optimal weight:    8.9990
   chunk 15 optimal weight:    0.9980
   chunk 30 optimal weight:    0.3980
   chunk 11 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 3 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.134856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.123982 restraints weight = 13848.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3883 rms_B_bonded: 1.70
r_work: 0.3816 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.3742 rms_B_bonded: 3.07 restraints_weight: 0.2500
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.5877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3522  Z= 0.134
  Angle     :  0.430   3.841   4710  Z= 0.221
  Chirality :  0.051   0.126    528
  Planarity :  0.003   0.036    600
  Dihedral  :  4.612  18.639    468
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 0.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 12.63 %
    Favored  : 85.61 %
  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: -1.17 (0.36), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.88 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS C 362 
 PHE   0.002   0.000   PHE A 346 
 TYR   0.006   0.001   TYR A 310 
 ARG   0.004   0.000   ARG B 379 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.627 
Fit side-chains
REVERT: A  314 ASP cc_start: 0.8133 (t0) cc_final: 0.7608 (t0)
REVERT: A  372 GLU cc_start: 0.8439 (tt0) cc_final: 0.8127 (tt0)
REVERT: B  340 LYS cc_start: 0.7736 (mtpp) cc_final: 0.6812 (mttm)
REVERT: B  369 LYS cc_start: 0.8685 (tttt) cc_final: 0.8201 (ttmm)
REVERT: B  375 LYS cc_start: 0.8355 (ttmt) cc_final: 0.8055 (tttm)
REVERT: C  348 ASP cc_start: 0.7457 (p0) cc_final: 0.6712 (p0)
REVERT: D  307 GLN cc_start: 0.8302 (tt0) cc_final: 0.7787 (mt0)
REVERT: D  336 GLN cc_start: 0.8453 (mt0) cc_final: 0.8194 (tt0)
REVERT: D  375 LYS cc_start: 0.8648 (ttmt) cc_final: 0.8400 (tttp)
REVERT: E  343 LYS cc_start: 0.7911 (mtpp) cc_final: 0.7556 (ttpp)
REVERT: F  307 GLN cc_start: 0.8000 (tt0) cc_final: 0.7519 (mt0)
REVERT: F  340 LYS cc_start: 0.7722 (ttpp) cc_final: 0.7098 (mmtt)
REVERT: F  375 LYS cc_start: 0.8601 (ttmt) cc_final: 0.8351 (tttm)
  outliers start: 7
  outliers final: 6
  residues processed: 74
  average time/residue: 0.5433
  time to fit residues: 45.7398
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  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  345 ASP
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain F residue  341 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    7.9990
   chunk 7 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0030
   overall best weight:    1.7996

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.131999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.121189 restraints weight = 14056.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3842 rms_B_bonded: 1.61
r_work: 0.3780 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3711 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.5953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3522  Z= 0.198
  Angle     :  0.455   3.868   4710  Z= 0.235
  Chirality :  0.050   0.123    528
  Planarity :  0.003   0.039    600
  Dihedral  :  4.676  18.522    468
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 1.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 13.38 %
    Favored  : 84.85 %
  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 (0.36), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.89 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS C 330 
 PHE   0.003   0.001   PHE C 346 
 TYR   0.004   0.001   TYR C 310 
 ARG   0.004   0.000   ARG B 379 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.636 
Fit side-chains
REVERT: A  314 ASP cc_start: 0.8164 (t0) cc_final: 0.7670 (t0)
REVERT: A  372 GLU cc_start: 0.8436 (tt0) cc_final: 0.8129 (tt0)
REVERT: B  340 LYS cc_start: 0.7838 (mtpp) cc_final: 0.6969 (mttm)
REVERT: B  369 LYS cc_start: 0.8698 (tttt) cc_final: 0.8241 (ttmm)
REVERT: B  375 LYS cc_start: 0.8401 (ttmt) cc_final: 0.8139 (tttm)
REVERT: D  307 GLN cc_start: 0.8286 (tt0) cc_final: 0.7809 (mt0)
REVERT: D  336 GLN cc_start: 0.8452 (mt0) cc_final: 0.8206 (tt0)
REVERT: D  375 LYS cc_start: 0.8676 (ttmt) cc_final: 0.8455 (tttp)
REVERT: E  343 LYS cc_start: 0.7985 (mtpp) cc_final: 0.7672 (ttpp)
REVERT: F  307 GLN cc_start: 0.7999 (tt0) cc_final: 0.7543 (mt0)
REVERT: F  324 SER cc_start: 0.8770 (m) cc_final: 0.8554 (t)
REVERT: F  340 LYS cc_start: 0.7727 (ttpp) cc_final: 0.7178 (mmtt)
REVERT: F  369 LYS cc_start: 0.8455 (ttmm) cc_final: 0.8020 (ttmm)
REVERT: F  375 LYS cc_start: 0.8584 (ttmt) cc_final: 0.8378 (tttm)
  outliers start: 7
  outliers final: 7
  residues processed: 74
  average time/residue: 0.5525
  time to fit residues: 46.8020
Evaluate side-chains
  72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  345 ASP
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain F residue  341 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 12 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 5 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 8 optimal weight:    4.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.132024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.121167 restraints weight = 14184.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3845 rms_B_bonded: 1.67
r_work: 0.3776 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.3705 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
moved from start:          0.6028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3522  Z= 0.185
  Angle     :  0.457   4.828   4710  Z= 0.238
  Chirality :  0.050   0.126    528
  Planarity :  0.003   0.037    600
  Dihedral  :  4.694  18.071    468
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 1.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 13.38 %
    Favored  : 84.85 %
  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: -1.20 (0.36), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.90 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS C 330 
 PHE   0.002   0.001   PHE C 346 
 TYR   0.005   0.001   TYR C 310 
 ARG   0.004   0.000   ARG B 379 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.579 
Fit side-chains
REVERT: A  314 ASP cc_start: 0.8137 (t0) cc_final: 0.7591 (t0)
REVERT: A  372 GLU cc_start: 0.8434 (tt0) cc_final: 0.8106 (tt0)
REVERT: B  340 LYS cc_start: 0.7806 (mtpp) cc_final: 0.6891 (mttm)
REVERT: B  369 LYS cc_start: 0.8695 (tttt) cc_final: 0.8199 (ttmm)
REVERT: B  375 LYS cc_start: 0.8379 (ttmt) cc_final: 0.8070 (tttm)
REVERT: D  307 GLN cc_start: 0.8319 (tt0) cc_final: 0.7773 (mt0)
REVERT: D  336 GLN cc_start: 0.8465 (mt0) cc_final: 0.8204 (tt0)
REVERT: D  375 LYS cc_start: 0.8689 (ttmt) cc_final: 0.8436 (tttp)
REVERT: E  343 LYS cc_start: 0.7971 (mtpp) cc_final: 0.7690 (ttpt)
REVERT: F  307 GLN cc_start: 0.8021 (tt0) cc_final: 0.7495 (mt0)
REVERT: F  324 SER cc_start: 0.8784 (m) cc_final: 0.8549 (t)
REVERT: F  340 LYS cc_start: 0.7720 (ttpp) cc_final: 0.7100 (mmtt)
REVERT: F  369 LYS cc_start: 0.8454 (ttmm) cc_final: 0.7996 (ttmm)
REVERT: F  375 LYS cc_start: 0.8548 (ttmt) cc_final: 0.8296 (tttm)
  outliers start: 7
  outliers final: 7
  residues processed: 74
  average time/residue: 0.5893
  time to fit residues: 49.7215
Evaluate side-chains
  74 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  345 ASP
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain F residue  341 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 24 optimal weight:    7.9990
   chunk 20 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 41 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.131233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.120412 restraints weight = 14006.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3837 rms_B_bonded: 1.69
r_work: 0.3767 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3696 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8577
moved from start:          0.6104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3522  Z= 0.192
  Angle     :  0.464   5.297   4710  Z= 0.242
  Chirality :  0.051   0.133    528
  Planarity :  0.003   0.037    600
  Dihedral  :  4.707  18.320    468
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 1.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 13.13 %
    Favored  : 84.85 %
  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: -1.21 (0.36), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.91 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS C 330 
 PHE   0.003   0.001   PHE C 346 
 TYR   0.005   0.001   TYR C 310 
 ARG   0.004   0.000   ARG B 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4731.55 seconds
wall clock time: 84 minutes 35.44 seconds (5075.44 seconds total)