Starting phenix.real_space_refine
on Wed Jun  4 16:28:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qkl_14046/06_2025/7qkl_14046.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qkl_14046/06_2025/7qkl_14046.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qkl_14046/06_2025/7qkl_14046.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qkl_14046/06_2025/7qkl_14046.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qkl_14046/06_2025/7qkl_14046.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qkl_14046/06_2025/7qkl_14046.cif"
  }
  resolution = 2.07
  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=   0.003
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: 4
    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
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 3468
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 578
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "B"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 578
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "C"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 578
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "D"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 578
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "E"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 578
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "F"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 578
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
  Time building chain proxies: 3.05, per 1000 atoms: 0.88
  Number of scatterers: 3468
  At special positions: 0
  Unit cell: (90.64, 135.136, 40.376, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       6     16.00
     O     648      8.00
     N     642      7.00
     C    2172      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.81
  Conformation dependent library (CDL) restraints added in 456.7 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 16 sheets defined
      0.0% alpha, 57.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310
      removed outlier: 6.474A  pdb=" N   GLN A 307 " --> pdb=" O   ILE C 308 " (cutoff:3.500A)
      removed outlier: 7.666A  pdb=" N   TYR C 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   VAL A 309 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314
      removed outlier: 6.771A  pdb=" N   VAL A 313 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 324
      removed outlier: 6.431A  pdb=" N   LYS A 317 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
      removed outlier: 8.089A  pdb=" N   SER C 320 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   THR A 319 " --> pdb=" O   SER C 320 " (cutoff:3.500A)
      removed outlier: 8.166A  pdb=" N   CYS C 322 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   LYS A 321 " --> pdb=" O   CYS C 322 " (cutoff:3.500A)
      removed outlier: 7.729A  pdb=" N   SER C 324 " --> pdb=" O   LYS A 321 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   GLY A 323 " --> pdb=" O   SER C 324 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330
      removed outlier: 6.447A  pdb=" N   HIS A 329 " --> pdb=" O   HIS C 330 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 347
      removed outlier: 5.967A  pdb=" N   VAL A 337 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
      removed outlier: 7.669A  pdb=" N   LYS C 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   VAL A 339 " --> pdb=" O   LYS C 340 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   GLU C 342 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   SER A 341 " --> pdb=" O   GLU C 342 " (cutoff:3.500A)
      removed outlier: 7.921A  pdb=" N   LEU C 344 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   LYS A 343 " --> pdb=" O   LEU C 344 " (cutoff:3.500A)
      removed outlier: 7.662A  pdb=" N   PHE C 346 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   ASP A 345 " --> pdb=" O   PHE C 346 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   VAL C 337 " --> pdb=" O   GLN B 336 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   GLU B 338 " --> pdb=" O   VAL C 337 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 354
      removed outlier: 6.581A  pdb=" N   GLN A 351 " --> pdb=" O   SER C 352 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   ILE C 354 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   LYS A 353 " --> pdb=" O   ILE C 354 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   VAL B 350 " --> pdb=" O   GLN C 351 " (cutoff:3.500A)
      removed outlier: 7.929A  pdb=" N   LYS C 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   SER B 352 " --> pdb=" O   LYS C 353 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 362
      removed outlier: 6.615A  pdb=" N   ASP A 358 " --> pdb=" O   ASN C 359 " (cutoff:3.500A)
      removed outlier: 7.848A  pdb=" N   THR C 361 " --> pdb=" O   ASP A 358 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ILE A 360 " --> pdb=" O   THR C 361 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   LEU B 357 " --> pdb=" O   ASP C 358 " (cutoff:3.500A)
      removed outlier: 7.722A  pdb=" N   ILE C 360 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   ASN B 359 " --> pdb=" O   ILE C 360 " (cutoff:3.500A)
      removed outlier: 7.847A  pdb=" N   HIS C 362 " --> pdb=" O   ASN B 359 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   THR B 361 " --> pdb=" O   HIS C 362 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 368 through 378
      removed outlier: 6.549A  pdb=" N   LYS A 369 " --> pdb=" O   LYS C 370 " (cutoff:3.500A)
      removed outlier: 7.913A  pdb=" N   GLU C 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   ILE A 371 " --> pdb=" O   GLU C 372 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   HIS C 374 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   THR A 373 " --> pdb=" O   HIS C 374 " (cutoff:3.500A)
      removed outlier: 7.963A  pdb=" N   LEU C 376 " --> pdb=" O   THR A 373 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   LYS A 375 " --> pdb=" O   LEU C 376 " (cutoff:3.500A)
      removed outlier: 7.889A  pdb=" N   PHE C 378 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   THR A 377 " --> pdb=" O   PHE C 378 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 306 through 310
      removed outlier: 6.410A  pdb=" N   GLN D 307 " --> pdb=" O   ILE F 308 " (cutoff:3.500A)
      removed outlier: 7.610A  pdb=" N   TYR F 310 " --> pdb=" O   GLN D 307 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   VAL D 309 " --> pdb=" O   TYR F 310 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 313 through 314
      removed outlier: 6.813A  pdb=" N   VAL D 313 " --> pdb=" O   ASP F 314 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 317 through 324
      removed outlier: 6.482A  pdb=" N   LYS D 317 " --> pdb=" O   VAL F 318 " (cutoff:3.500A)
      removed outlier: 8.123A  pdb=" N   SER F 320 " --> pdb=" O   LYS D 317 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   THR D 319 " --> pdb=" O   SER F 320 " (cutoff:3.500A)
      removed outlier: 8.177A  pdb=" N   CYS F 322 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   LYS D 321 " --> pdb=" O   CYS F 322 " (cutoff:3.500A)
      removed outlier: 7.795A  pdb=" N   SER F 324 " --> pdb=" O   LYS D 321 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   GLY D 323 " --> pdb=" O   SER F 324 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   VAL E 318 " --> pdb=" O   THR F 319 " (cutoff:3.500A)
      removed outlier: 8.009A  pdb=" N   LYS F 321 " --> pdb=" O   VAL E 318 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   SER E 320 " --> pdb=" O   LYS F 321 " (cutoff:3.500A)
      removed outlier: 7.902A  pdb=" N   GLY F 323 " --> pdb=" O   SER E 320 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   CYS E 322 " --> pdb=" O   GLY F 323 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'D' and resid 328 through 330
      removed outlier: 6.467A  pdb=" N   HIS D 329 " --> pdb=" O   HIS F 330 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   ILE E 328 " --> pdb=" O   HIS F 329 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'D' and resid 336 through 347
      removed outlier: 6.997A  pdb=" N   VAL D 337 " --> pdb=" O   GLN F 336 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   GLU F 338 " --> pdb=" O   VAL D 337 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   VAL F 337 " --> pdb=" O   GLN E 336 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   GLU E 338 " --> pdb=" O   VAL F 337 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 350 through 354
      removed outlier: 6.212A  pdb=" N   VAL E 350 " --> pdb=" O   GLN F 351 " (cutoff:3.500A)
      removed outlier: 7.926A  pdb=" N   LYS F 353 " --> pdb=" O   VAL E 350 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   SER E 352 " --> pdb=" O   LYS F 353 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 357 through 362
      removed outlier: 6.580A  pdb=" N   ASP D 358 " --> pdb=" O   ASN F 359 " (cutoff:3.500A)
      removed outlier: 7.781A  pdb=" N   THR F 361 " --> pdb=" O   ASP D 358 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ILE D 360 " --> pdb=" O   THR F 361 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   LEU E 357 " --> pdb=" O   ASP F 358 " (cutoff:3.500A)
      removed outlier: 7.734A  pdb=" N   ILE F 360 " --> pdb=" O   LEU E 357 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   ASN E 359 " --> pdb=" O   ILE F 360 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   HIS F 362 " --> pdb=" O   ASN E 359 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   THR E 361 " --> pdb=" O   HIS F 362 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'D' and resid 368 through 378
      removed outlier: 6.537A  pdb=" N   LYS D 369 " --> pdb=" O   LYS F 370 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   GLU F 372 " --> pdb=" O   LYS D 369 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   ILE D 371 " --> pdb=" O   GLU F 372 " (cutoff:3.500A)
      removed outlier: 7.996A  pdb=" N   HIS F 374 " --> pdb=" O   ILE D 371 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   THR D 373 " --> pdb=" O   HIS F 374 " (cutoff:3.500A)
      removed outlier: 7.971A  pdb=" N   LEU F 376 " --> pdb=" O   THR D 373 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   LYS D 375 " --> pdb=" O   LEU F 376 " (cutoff:3.500A)
      removed outlier: 7.761A  pdb=" N   PHE F 378 " --> pdb=" O   LYS D 375 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   THR D 377 " --> pdb=" O   PHE F 378 " (cutoff:3.500A)

    70 hydrogen bonds defined for protein.
    210 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: 0.73

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 1064
        1.34 -     1.46: 410
        1.46 -     1.58: 2041
        1.58 -     1.70: 1
        1.70 -     1.82: 6
  Bond restraints: 3522
  Sorted by residual:
  bond pdb=" CB  VAL C 339 "
       pdb=" CG2 VAL C 339 "
    ideal  model  delta    sigma   weight residual
    1.521  1.618 -0.097 3.30e-02 9.18e+02 8.62e+00
  bond pdb=" CZ  ARG C 349 "
       pdb=" NH2 ARG C 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.05e+00
  bond pdb=" CZ  ARG A 349 "
       pdb=" NH2 ARG A 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 5.89e+00
  bond pdb=" CZ  ARG F 349 "
       pdb=" NH2 ARG F 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.75e+00
  bond pdb=" CZ  ARG D 349 "
       pdb=" NH2 ARG D 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.70e+00
  ... (remaining 3517 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.41: 4575
        4.41 -     8.83: 105
        8.83 -    13.24: 1
       13.24 -    17.66: 9
       17.66 -    22.07: 20
  Bond angle restraints: 4710
  Sorted by residual:
  angle pdb=" CA  VAL D 309 "
        pdb=" CB  VAL D 309 "
        pdb=" CG1 VAL D 309 "
      ideal   model   delta    sigma   weight residual
     110.40  132.47  -22.07 1.70e+00 3.46e-01 1.69e+02
  angle pdb=" CA  VAL A 313 "
        pdb=" CB  VAL A 313 "
        pdb=" CG1 VAL A 313 "
      ideal   model   delta    sigma   weight residual
     110.40  132.46  -22.06 1.70e+00 3.46e-01 1.68e+02
  angle pdb=" CA  VAL A 309 "
        pdb=" CB  VAL A 309 "
        pdb=" CG1 VAL A 309 "
      ideal   model   delta    sigma   weight residual
     110.40  132.43  -22.03 1.70e+00 3.46e-01 1.68e+02
  angle pdb=" CA  VAL D 318 "
        pdb=" CB  VAL D 318 "
        pdb=" CG1 VAL D 318 "
      ideal   model   delta    sigma   weight residual
     110.40  131.78  -21.38 1.70e+00 3.46e-01 1.58e+02
  angle pdb=" CA  VAL B 309 "
        pdb=" CB  VAL B 309 "
        pdb=" CG1 VAL B 309 "
      ideal   model   delta    sigma   weight residual
     110.40  131.71  -21.31 1.70e+00 3.46e-01 1.57e+02
  ... (remaining 4705 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.14: 1994
       17.14 -    34.27: 110
       34.27 -    51.40: 21
       51.40 -    68.53: 11
       68.53 -    85.67: 6
  Dihedral angle restraints: 2142
    sinusoidal: 894
      harmonic: 1248
  Sorted by residual:
  dihedral pdb=" CA  LYS C 347 "
           pdb=" C   LYS C 347 "
           pdb=" N   ASP C 348 "
           pdb=" CA  ASP C 348 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.93   20.07     0      5.00e+00 4.00e-02 1.61e+01
  dihedral pdb=" CA  LYS F 347 "
           pdb=" C   LYS F 347 "
           pdb=" N   ASP F 348 "
           pdb=" CA  ASP F 348 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.65   19.35     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" C   VAL C 337 "
           pdb=" N   VAL C 337 "
           pdb=" CA  VAL C 337 "
           pdb=" CB  VAL C 337 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -131.33    9.33     0      2.50e+00 1.60e-01 1.39e+01
  ... (remaining 2139 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.249: 489
       0.249 -    0.498: 9
       0.498 -    0.747: 5
       0.747 -    0.996: 14
       0.996 -    1.246: 11
  Chirality restraints: 528
  Sorted by residual:
  chirality pdb=" CB  VAL C 313 "
            pdb=" CA  VAL C 313 "
            pdb=" CG1 VAL C 313 "
            pdb=" CG2 VAL C 313 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.38   -1.25 2.00e-01 2.50e+01 3.88e+01
  chirality pdb=" CB  VAL C 318 "
            pdb=" CA  VAL C 318 "
            pdb=" CG1 VAL C 318 "
            pdb=" CG2 VAL C 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.42   -1.21 2.00e-01 2.50e+01 3.67e+01
  chirality pdb=" CB  VAL A 309 "
            pdb=" CA  VAL A 309 "
            pdb=" CG1 VAL A 309 "
            pdb=" CG2 VAL A 309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.45   -1.18 2.00e-01 2.50e+01 3.46e+01
  ... (remaining 525 not shown)

  Planarity restraints: 600
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 310 "   -0.058 2.00e-02 2.50e+03   3.30e-02 2.17e+01
        pdb=" CG  TYR C 310 "    0.019 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 310 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 310 "    0.027 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 310 "    0.021 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 310 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 310 "    0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR C 310 "   -0.055 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 310 "   -0.038 2.00e-02 2.50e+03   2.41e-02 1.16e+01
        pdb=" CG  TYR A 310 "    0.007 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 310 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 310 "    0.014 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 310 "    0.017 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 310 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 310 "    0.013 2.00e-02 2.50e+03
        pdb=" OH  TYR A 310 "   -0.045 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS F 330 "    0.034 2.00e-02 2.50e+03   2.56e-02 9.80e+00
        pdb=" CG  HIS F 330 "   -0.039 2.00e-02 2.50e+03
        pdb=" ND1 HIS F 330 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 HIS F 330 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 HIS F 330 "    0.019 2.00e-02 2.50e+03
        pdb=" NE2 HIS F 330 "    0.018 2.00e-02 2.50e+03
  ... (remaining 597 not shown)

  Histogram of nonbonded interaction distances:
        2.54 -     3.01: 1698
        3.01 -     3.48: 2830
        3.48 -     3.95: 5551
        3.95 -     4.43: 5560
        4.43 -     4.90: 10503
  Nonbonded interactions: 26142
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP F 314 "
            pdb=" OG  SER F 316 "
     model   vdw
     2.537 3.040
  nonbonded pdb=" OD1 ASP A 314 "
            pdb=" OG  SER A 316 "
     model   vdw
     2.545 3.040
  nonbonded pdb=" OD1 ASP C 314 "
            pdb=" OG  SER C 316 "
     model   vdw
     2.545 3.040
  nonbonded pdb=" OD1 ASP D 314 "
            pdb=" OG  SER D 316 "
     model   vdw
     2.555 3.040
  nonbonded pdb=" OD1 ASP E 314 "
            pdb=" OG  SER E 316 "
     model   vdw
     2.559 3.040
  ... (remaining 26137 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.430
  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:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.510
  Find NCS groups from input model:        0.130
  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:             0.000
  Load rotamer database and sin/cos tables:17.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
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   0.097   3522  Z= 0.675
  Angle     :  2.367  22.071   4710  Z= 1.491
  Chirality :  0.248   1.246    528
  Planarity :  0.009   0.050    600
  Dihedral  : 12.790  85.668   1350
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 0.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  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: -1.75 (0.32), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.33 (0.25), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS B 330 
 PHE   0.030   0.009   PHE B 378 
 TYR   0.058   0.012   TYR C 310 
 ARG   0.003   0.001   ARG C 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05666 (   70)
  hydrogen bonds       : angle       8.18498 (  210)
  covalent geometry    : bond        0.01126 ( 3522)
  covalent geometry    : angle       2.36723 ( 4710)

*********************** 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
  218 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  343 LYS cc_start: 0.6820 (tptm) cc_final: 0.6506 (mptp)
REVERT: A  345 ASP cc_start: 0.7368 (t0) cc_final: 0.6655 (m-30)
REVERT: A  349 ARG cc_start: 0.7184 (mtt-85) cc_final: 0.6708 (mtm180)
REVERT: B  343 LYS cc_start: 0.7418 (tptm) cc_final: 0.7041 (mtmt)
REVERT: C  343 LYS cc_start: 0.6950 (tptm) cc_final: 0.6334 (mptp)
REVERT: C  349 ARG cc_start: 0.7092 (mtt-85) cc_final: 0.6874 (mtm180)
REVERT: D  343 LYS cc_start: 0.6878 (tptm) cc_final: 0.6289 (tmmt)
REVERT: D  360 ILE cc_start: 0.8825 (mp) cc_final: 0.8590 (mt)
REVERT: E  320 SER cc_start: 0.8785 (t) cc_final: 0.8535 (p)
REVERT: E  343 LYS cc_start: 0.7573 (tptm) cc_final: 0.6969 (mptt)
REVERT: E  348 ASP cc_start: 0.7159 (t0) cc_final: 0.6876 (t0)
REVERT: F  343 LYS cc_start: 0.6980 (tptm) cc_final: 0.6460 (mptp)
REVERT: F  345 ASP cc_start: 0.7302 (t0) cc_final: 0.7055 (t0)
REVERT: F  349 ARG cc_start: 0.7080 (mtt-85) cc_final: 0.6587 (mtm180)
REVERT: F  353 LYS cc_start: 0.8307 (mttt) cc_final: 0.8020 (mttt)
  outliers start: 0
  outliers final: 0
  residues processed: 218
  average time/residue: 1.2851
  time to fit residues: 286.7110
Evaluate side-chains
  149 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 31 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 32 optimal weight:    5.9990
   chunk 12 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
B 307 GLN
B 359 ASN
C 351 GLN
C 359 ASN
D 359 ASN
E 351 GLN
E 359 ASN
F 359 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.144751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.131165 restraints weight = 2946.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3829 rms_B_bonded: 1.00
r_work: 0.3740 rms_B_bonded: 1.15 restraints_weight: 0.5000
r_work: 0.3651 rms_B_bonded: 2.03 restraints_weight: 0.2500
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8739
moved from start:          0.2921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   3522  Z= 0.097
  Angle     :  0.596   7.213   4710  Z= 0.276
  Chirality :  0.049   0.128    528
  Planarity :  0.003   0.020    600
  Dihedral  :  4.511  17.117    468
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 2.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 19.95 %
    Favored  : 79.55 %
  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: -1.25 (0.34), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.94 (0.26), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A 362 
 PHE   0.008   0.002   PHE E 346 
 TYR   0.008   0.001   TYR B 310 
 ARG   0.004   0.000   ARG C 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01674 (   70)
  hydrogen bonds       : angle       5.72115 (  210)
  covalent geometry    : bond        0.00217 ( 3522)
  covalent geometry    : angle       0.59618 ( 4710)

*********************** 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
  156 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 154
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
REVERT: C  343 LYS cc_start: 0.7901 (tptm) cc_final: 0.7689 (tmmt)
REVERT: D  307 GLN cc_start: 0.8485 (tt0) cc_final: 0.8274 (tt0)
REVERT: E  379 ARG cc_start: 0.6441 (mmt180) cc_final: 0.6233 (mtp85)
  outliers start: 2
  outliers final: 0
  residues processed: 154
  average time/residue: 1.5979
  time to fit residues: 251.0410
Evaluate side-chains
  117 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 28 optimal weight:   10.0000
   chunk 17 optimal weight:    9.9990
   chunk 21 optimal weight:   10.0000
   chunk 26 optimal weight:    9.9990
   chunk 35 optimal weight:    3.9990
   chunk 8 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9990
   chunk 7 optimal weight:   10.0000
   chunk 1 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
C 351 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.140606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.127456 restraints weight = 3013.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3776 rms_B_bonded: 1.00
r_work: 0.3684 rms_B_bonded: 1.15 restraints_weight: 0.5000
r_work: 0.3595 rms_B_bonded: 2.03 restraints_weight: 0.2500
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8797
moved from start:          0.3714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3522  Z= 0.114
  Angle     :  0.568   6.330   4710  Z= 0.267
  Chirality :  0.050   0.123    528
  Planarity :  0.003   0.022    600
  Dihedral  :  4.492  16.415    468
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 21.72 %
    Favored  : 77.78 %
  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: -1.13 (0.35), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.85 (0.26), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS E 374 
 PHE   0.006   0.002   PHE D 346 
 TYR   0.007   0.002   TYR B 310 
 ARG   0.004   0.001   ARG F 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01834 (   70)
  hydrogen bonds       : angle       5.38707 (  210)
  covalent geometry    : bond        0.00260 ( 3522)
  covalent geometry    : angle       0.56771 ( 4710)

*********************** 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
  120 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 118
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
REVERT: D  343 LYS cc_start: 0.8208 (mptp) cc_final: 0.7827 (tmmt)
REVERT: E  379 ARG cc_start: 0.6429 (mmt180) cc_final: 0.6227 (mtp85)
  outliers start: 2
  outliers final: 0
  residues processed: 118
  average time/residue: 1.6138
  time to fit residues: 194.8147
Evaluate side-chains
  103 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 14 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 24 optimal weight:    7.9990
   chunk 39 optimal weight:    4.9990
   chunk 0 optimal weight:    0.8980
   chunk 32 optimal weight:    7.9990
   chunk 22 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   chunk 17 optimal weight:    8.9990
   overall best weight:    3.5786

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

Flipped N/Q/H residues before XYZ refinement:
C 351 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.139644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.127183 restraints weight = 3138.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 0.93
r_work: 0.3652 rms_B_bonded: 1.07 restraints_weight: 0.5000
r_work: 0.3565 rms_B_bonded: 1.88 restraints_weight: 0.2500
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8823
moved from start:          0.3930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   3522  Z= 0.191
  Angle     :  0.615   5.992   4710  Z= 0.301
  Chirality :  0.052   0.143    528
  Planarity :  0.003   0.038    600
  Dihedral  :  4.831  17.758    468
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 19.95 %
    Favored  : 79.04 %
  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: -1.19 (0.35), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.90 (0.26), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 374 
 PHE   0.007   0.002   PHE D 346 
 TYR   0.008   0.002   TYR F 310 
 ARG   0.006   0.001   ARG F 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02365 (   70)
  hydrogen bonds       : angle       5.59108 (  210)
  covalent geometry    : bond        0.00432 ( 3522)
  covalent geometry    : angle       0.61477 ( 4710)

*********************** 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
  107 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 103
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
REVERT: E  379 ARG cc_start: 0.6445 (mmt180) cc_final: 0.6225 (mtp85)
REVERT: F  343 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7970 (tmtm)
  outliers start: 4
  outliers final: 1
  residues processed: 104
  average time/residue: 1.3763
  time to fit residues: 146.6715
Evaluate side-chains
  108 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 106
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  342 GLU
Chi-restraints excluded: chain F residue  343 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 23 optimal weight:    9.9990
   chunk 30 optimal weight:    0.0770
   chunk 41 optimal weight:   10.0000
   chunk 35 optimal weight:    8.9990
   chunk 19 optimal weight:   10.0000
   chunk 15 optimal weight:    9.9990
   chunk 13 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    3.4146

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

Flipped N/Q/H residues before XYZ refinement:
C 351 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.138529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.125161 restraints weight = 3024.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 1.02
r_work: 0.3640 rms_B_bonded: 1.15 restraints_weight: 0.5000
r_work: 0.3550 rms_B_bonded: 2.02 restraints_weight: 0.2500
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8837
moved from start:          0.4018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3522  Z= 0.184
  Angle     :  0.597   5.734   4710  Z= 0.291
  Chirality :  0.051   0.131    528
  Planarity :  0.003   0.032    600
  Dihedral  :  4.829  18.114    468
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 20.45 %
    Favored  : 79.04 %
  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 A 362 
 PHE   0.007   0.002   PHE D 378 
 TYR   0.008   0.002   TYR B 310 
 ARG   0.004   0.001   ARG F 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02362 (   70)
  hydrogen bonds       : angle       5.49413 (  210)
  covalent geometry    : bond        0.00416 ( 3522)
  covalent geometry    : angle       0.59699 ( 4710)

*********************** 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
  104 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 102
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
REVERT: E  379 ARG cc_start: 0.6399 (mmt180) cc_final: 0.6197 (mtp85)
  outliers start: 2
  outliers final: 1
  residues processed: 103
  average time/residue: 1.4597
  time to fit residues: 153.7990
Evaluate side-chains
  103 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  315 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    9.9990
   chunk 3 optimal weight:    4.9990
   chunk 27 optimal weight:    0.3980
   chunk 30 optimal weight:    0.0060
   chunk 39 optimal weight:   10.0000
   chunk 6 optimal weight:    0.0770
   chunk 38 optimal weight:    9.9990
   chunk 34 optimal weight:   10.0000
   chunk 2 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9980
   overall best weight:    1.2956

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

Flipped N/Q/H residues before XYZ refinement:
C 351 GLN
D 307 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.140605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.127282 restraints weight = 3025.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3758 rms_B_bonded: 1.02
r_work: 0.3668 rms_B_bonded: 1.15 restraints_weight: 0.5000
r_work: 0.3579 rms_B_bonded: 2.02 restraints_weight: 0.2500
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8812
moved from start:          0.4062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   3522  Z= 0.097
  Angle     :  0.518   5.017   4710  Z= 0.245
  Chirality :  0.049   0.123    528
  Planarity :  0.002   0.030    600
  Dihedral  :  4.479  16.616    468
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 20.45 %
    Favored  : 78.79 %
  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   0.001   0.000   HIS A 362 
 PHE   0.005   0.001   PHE D 378 
 TYR   0.006   0.001   TYR B 310 
 ARG   0.007   0.001   ARG F 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01724 (   70)
  hydrogen bonds       : angle       5.08942 (  210)
  covalent geometry    : bond        0.00216 ( 3522)
  covalent geometry    : angle       0.51796 ( 4710)

*********************** 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
  111 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 108
  time to evaluate  : 0.441 
Fit side-chains
REVERT: D  331 LYS cc_start: 0.8807 (tttm) cc_final: 0.8367 (mmtm)
REVERT: D  342 GLU cc_start: 0.7871 (tt0) cc_final: 0.7513 (mt-10)
REVERT: D  343 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7818 (mptp)
REVERT: E  379 ARG cc_start: 0.6449 (mmt180) cc_final: 0.6236 (mtp85)
  outliers start: 3
  outliers final: 1
  residues processed: 109
  average time/residue: 1.5268
  time to fit residues: 170.1014
Evaluate side-chains
  111 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 109
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  343 LYS
Chi-restraints excluded: chain E residue  341 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 10 optimal weight:    0.7980
   chunk 37 optimal weight:   20.0000
   chunk 23 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 32 optimal weight:    9.9990
   chunk 13 optimal weight:    2.9990
   chunk 1 optimal weight:    8.9990
   chunk 17 optimal weight:    9.9990
   chunk 31 optimal weight:    0.1980
   overall best weight:    1.1582

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.142323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.129754 restraints weight = 3158.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3769 rms_B_bonded: 0.96
r_work: 0.3679 rms_B_bonded: 1.11 restraints_weight: 0.5000
r_work: 0.3593 rms_B_bonded: 1.96 restraints_weight: 0.2500
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8797
moved from start:          0.4099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   3522  Z= 0.091
  Angle     :  0.506   4.709   4710  Z= 0.239
  Chirality :  0.049   0.121    528
  Planarity :  0.002   0.018    600
  Dihedral  :  4.343  15.615    468
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  : 20.96 %
    Favored  : 78.79 %
  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: -1.25 (0.35), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.94 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A 362 
 PHE   0.004   0.001   PHE D 378 
 TYR   0.006   0.001   TYR B 310 
 ARG   0.004   0.000   ARG D 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01610 (   70)
  hydrogen bonds       : angle       4.88305 (  210)
  covalent geometry    : bond        0.00204 ( 3522)
  covalent geometry    : angle       0.50591 ( 4710)

*********************** 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
  110 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 109
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
REVERT: D  331 LYS cc_start: 0.8800 (tttm) cc_final: 0.8375 (mmtm)
REVERT: D  342 GLU cc_start: 0.7861 (tt0) cc_final: 0.7521 (mt-10)
REVERT: D  343 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7798 (tmmt)
REVERT: E  379 ARG cc_start: 0.6460 (mmt180) cc_final: 0.6242 (mtp85)
  outliers start: 1
  outliers final: 0
  residues processed: 109
  average time/residue: 1.5057
  time to fit residues: 167.7722
Evaluate side-chains
  108 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  343 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 25 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:    7.9990
   chunk 16 optimal weight:    0.1980
   chunk 32 optimal weight:    8.9990
   chunk 2 optimal weight:    1.9990
   chunk 21 optimal weight:   10.0000
   chunk 1 optimal weight:    7.9990
   chunk 4 optimal weight:    0.0770
   overall best weight:    2.0544

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.140865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.128277 restraints weight = 3132.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.3755 rms_B_bonded: 0.96
r_work: 0.3663 rms_B_bonded: 1.11 restraints_weight: 0.5000
r_work: 0.3574 rms_B_bonded: 1.96 restraints_weight: 0.2500
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8813
moved from start:          0.4080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3522  Z= 0.124
  Angle     :  0.531   4.778   4710  Z= 0.256
  Chirality :  0.049   0.124    528
  Planarity :  0.003   0.024    600
  Dihedral  :  4.554  16.390    468
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 20.71 %
    Favored  : 78.79 %
  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: -1.24 (0.35), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.94 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 362 
 PHE   0.005   0.001   PHE F 346 
 TYR   0.007   0.002   TYR B 310 
 ARG   0.004   0.001   ARG F 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01912 (   70)
  hydrogen bonds       : angle       4.98203 (  210)
  covalent geometry    : bond        0.00278 ( 3522)
  covalent geometry    : angle       0.53126 ( 4710)

*********************** 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
  109 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 107
  time to evaluate  : 0.440 
Fit side-chains
REVERT: D  331 LYS cc_start: 0.8831 (tttm) cc_final: 0.8423 (mmtm)
REVERT: D  342 GLU cc_start: 0.7887 (tt0) cc_final: 0.7533 (mt-10)
REVERT: D  343 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7589 (mptp)
  outliers start: 2
  outliers final: 0
  residues processed: 107
  average time/residue: 1.4765
  time to fit residues: 161.6182
Evaluate side-chains
  108 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  343 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 36 optimal weight:    9.9990
   chunk 10 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0030
   chunk 25 optimal weight:    8.9990
   chunk 26 optimal weight:    3.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    2.9998

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.139740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.127134 restraints weight = 3090.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3740 rms_B_bonded: 0.95
r_work: 0.3648 rms_B_bonded: 1.10 restraints_weight: 0.5000
r_work: 0.3560 rms_B_bonded: 1.93 restraints_weight: 0.2500
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8823
moved from start:          0.4015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3522  Z= 0.165
  Angle     :  0.566   4.927   4710  Z= 0.278
  Chirality :  0.050   0.130    528
  Planarity :  0.003   0.035    600
  Dihedral  :  4.768  17.151    468
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  : 20.45 %
    Favored  : 79.29 %
  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: -1.27 (0.35), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.96 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 362 
 PHE   0.005   0.002   PHE E 378 
 TYR   0.008   0.002   TYR B 310 
 ARG   0.007   0.001   ARG D 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02228 (   70)
  hydrogen bonds       : angle       5.18565 (  210)
  covalent geometry    : bond        0.00373 ( 3522)
  covalent geometry    : angle       0.56553 ( 4710)

*********************** 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
  107 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 106
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
REVERT: D  343 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7614 (mptp)
  outliers start: 1
  outliers final: 0
  residues processed: 106
  average time/residue: 1.4557
  time to fit residues: 157.8513
Evaluate side-chains
  107 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 106
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  343 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 38 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 29 optimal weight:   10.0000
   chunk 24 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 19 optimal weight:   10.0000
   chunk 4 optimal weight:    0.0970
   chunk 39 optimal weight:   10.0000
   chunk 22 optimal weight:    8.9990
   chunk 16 optimal weight:    1.9990
   chunk 40 optimal weight:    9.9990
   overall best weight:    2.4186

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.139259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.125921 restraints weight = 3015.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3742 rms_B_bonded: 1.02
r_work: 0.3649 rms_B_bonded: 1.16 restraints_weight: 0.5000
r_work: 0.3557 rms_B_bonded: 2.04 restraints_weight: 0.2500
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8828
moved from start:          0.4078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3522  Z= 0.140
  Angle     :  0.545   4.740   4710  Z= 0.265
  Chirality :  0.049   0.126    528
  Planarity :  0.003   0.035    600
  Dihedral  :  4.697  17.264    468
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  : 21.21 %
    Favored  : 78.54 %
  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 (0.35), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.98 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 362 
 PHE   0.005   0.001   PHE F 346 
 TYR   0.008   0.002   TYR B 310 
 ARG   0.008   0.001   ARG D 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02034 (   70)
  hydrogen bonds       : angle       5.07953 (  210)
  covalent geometry    : bond        0.00316 ( 3522)
  covalent geometry    : angle       0.54495 ( 4710)

********************** 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
  107 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 106
  time to evaluate  : 0.467 
Fit side-chains
   revert: symmetry clash
REVERT: D  342 GLU cc_start: 0.7916 (tt0) cc_final: 0.7576 (mt-10)
REVERT: D  343 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7588 (mptp)
  outliers start: 1
  outliers final: 0
  residues processed: 106
  average time/residue: 1.4589
  time to fit residues: 158.2480
Evaluate side-chains
  107 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 106
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  343 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 22 optimal weight:    8.9990
   chunk 37 optimal weight:   20.0000
   chunk 35 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0870
   chunk 27 optimal weight:    3.9990
   overall best weight:    2.1964

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.139457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.126094 restraints weight = 3008.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 1.02
r_work: 0.3651 rms_B_bonded: 1.16 restraints_weight: 0.5000
r_work: 0.3560 rms_B_bonded: 2.03 restraints_weight: 0.2500
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8825
moved from start:          0.4039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3522  Z= 0.132
  Angle     :  0.539   4.782   4710  Z= 0.262
  Chirality :  0.049   0.126    528
  Planarity :  0.003   0.037    600
  Dihedral  :  4.671  17.155    468
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  : 20.96 %
    Favored  : 78.79 %
  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 (0.35), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.98 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 362 
 PHE   0.005   0.001   PHE F 346 
 TYR   0.007   0.002   TYR B 310 
 ARG   0.007   0.001   ARG D 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01984 (   70)
  hydrogen bonds       : angle       5.05492 (  210)
  covalent geometry    : bond        0.00296 ( 3522)
  covalent geometry    : angle       0.53948 ( 4710)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5001.18 seconds
wall clock time: 85 minutes 44.09 seconds (5144.09 seconds total)