Starting phenix.real_space_refine
on Tue Feb 11 04:25:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p66_13219/02_2025/7p66_13219.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p66_13219/02_2025/7p66_13219.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p66_13219/02_2025/7p66_13219.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p66_13219/02_2025/7p66_13219.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p66_13219/02_2025/7p66_13219.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p66_13219/02_2025/7p66_13219.cif"
  }
  resolution = 3.0
  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=   0.004
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      10      5.16       5
     C    2530      2.51       5
     N     760      2.21       5
     O     760      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 4060
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 812
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 4, 'TRANS': 103}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 2.71, per 1000 atoms: 0.67
  Number of scatterers: 4060
  At special positions: 0
  Unit cell: (109.25, 92, 46, 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      10     16.00
     O     760      8.00
     N     760      7.00
     C    2530      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: 0.89
  Conformation dependent library (CDL) restraints added in 517.5 milliseconds
  

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  930

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 44.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 275 through 284
      removed outlier: 6.877A  pdb=" N   GLN C 276 " --> pdb=" O   VAL B 275 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   ILE B 277 " --> pdb=" O   GLN C 276 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   ILE C 278 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   ASN B 279 " --> pdb=" O   ILE C 278 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   LYS C 280 " --> pdb=" O   ASN B 279 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   LYS B 281 " --> pdb=" O   LYS C 280 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   GLN A 276 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
      removed outlier: 7.909A  pdb=" N   ASN B 279 " --> pdb=" O   GLN A 276 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   ILE A 278 " --> pdb=" O   ASN B 279 " (cutoff:3.500A)
      removed outlier: 7.949A  pdb=" N   LYS B 281 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 8.444A  pdb=" N   LYS A 280 " --> pdb=" O   LYS B 281 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   ASP B 283 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
      removed outlier: 9.324A  pdb=" N   LEU A 282 " --> pdb=" O   ASP B 283 " (cutoff:3.500A)
      removed outlier: 8.963A  pdb=" N   GLN A 276 " --> pdb=" O   ILE D 277 " (cutoff:3.500A)
      removed outlier: 10.331A  pdb=" N   ASN D 279 " --> pdb=" O   GLN A 276 " (cutoff:3.500A)
      removed outlier: 9.178A  pdb=" N   ILE A 278 " --> pdb=" O   ASN D 279 " (cutoff:3.500A)
      removed outlier: 10.215A  pdb=" N   LYS D 281 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   LYS A 280 " --> pdb=" O   LYS D 281 " (cutoff:3.500A)
      removed outlier: 8.603A  pdb=" N   ASP D 283 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   LEU A 282 " --> pdb=" O   ASP D 283 " (cutoff:3.500A)
      removed outlier: 8.952A  pdb=" N   GLN D 276 " --> pdb=" O   ILE E 277 " (cutoff:3.500A)
      removed outlier: 10.315A  pdb=" N   ASN E 279 " --> pdb=" O   GLN D 276 " (cutoff:3.500A)
      removed outlier: 9.162A  pdb=" N   ILE D 278 " --> pdb=" O   ASN E 279 " (cutoff:3.500A)
      removed outlier: 10.191A  pdb=" N   LYS E 281 " --> pdb=" O   ILE D 278 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   LYS D 280 " --> pdb=" O   LYS E 281 " (cutoff:3.500A)
      removed outlier: 8.583A  pdb=" N   ASP E 283 " --> pdb=" O   LYS D 280 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   LEU D 282 " --> pdb=" O   ASP E 283 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 287 through 290
      removed outlier: 6.333A  pdb=" N   VAL A 287 " --> pdb=" O   GLN D 288 " (cutoff:3.500A)
      removed outlier: 8.113A  pdb=" N   LYS D 290 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   SER A 289 " --> pdb=" O   LYS D 290 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   VAL D 287 " --> pdb=" O   GLN E 288 " (cutoff:3.500A)
      removed outlier: 8.111A  pdb=" N   LYS E 290 " --> pdb=" O   VAL D 287 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   SER D 289 " --> pdb=" O   LYS E 290 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 297 through 298
      removed outlier: 6.690A  pdb=" N   ILE A 297 " --> pdb=" O   LYS D 298 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   ILE D 297 " --> pdb=" O   LYS E 298 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 306 through 310
      removed outlier: 6.531A  pdb=" N   GLN A 307 " --> pdb=" O   ILE D 308 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   TYR D 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   VAL A 309 " --> pdb=" O   TYR D 310 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   GLN D 307 " --> pdb=" O   ILE E 308 " (cutoff:3.500A)
      removed outlier: 7.741A  pdb=" N   TYR E 310 " --> pdb=" O   GLN D 307 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   VAL D 309 " --> pdb=" O   TYR E 310 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 313 through 314
      removed outlier: 6.804A  pdb=" N   VAL B 313 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   VAL A 313 " --> pdb=" O   ASP B 314 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 317 through 322
      removed outlier: 6.334A  pdb=" N   VAL A 318 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
      removed outlier: 7.900A  pdb=" N   LYS D 321 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   SER A 320 " --> pdb=" O   LYS D 321 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   VAL D 318 " --> pdb=" O   THR E 319 " (cutoff:3.500A)
      removed outlier: 7.902A  pdb=" N   LYS E 321 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   SER D 320 " --> pdb=" O   LYS E 321 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 328 through 330
      removed outlier: 6.420A  pdb=" N   ILE A 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   ILE D 328 " --> pdb=" O   HIS E 329 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 337 through 345
      removed outlier: 6.542A  pdb=" N   GLU B 338 " --> pdb=" O   VAL C 339 " (cutoff:3.500A)
      removed outlier: 7.946A  pdb=" N   SER C 341 " --> pdb=" O   GLU B 338 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   LYS B 340 " --> pdb=" O   SER C 341 " (cutoff:3.500A)
      removed outlier: 7.960A  pdb=" N   LYS C 343 " --> pdb=" O   LYS B 340 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   GLU B 342 " --> pdb=" O   LYS C 343 " (cutoff:3.500A)
      removed outlier: 7.731A  pdb=" N   ASP C 345 " --> pdb=" O   GLU B 342 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LEU B 344 " --> pdb=" O   ASP C 345 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 348 through 350
      removed outlier: 6.995A  pdb=" N   ASP B 348 " --> pdb=" O   ARG C 349 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   ASP A 348 " --> pdb=" O   ARG B 349 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 355 through 362
      removed outlier: 6.929A  pdb=" N   SER B 356 " --> pdb=" O   GLY C 355 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   LEU C 357 " --> pdb=" O   SER B 356 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   ASP B 358 " --> pdb=" O   LEU C 357 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   ASN C 359 " --> pdb=" O   ASP B 358 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   SER A 356 " --> pdb=" O   GLY B 355 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   LEU B 357 " --> pdb=" O   SER A 356 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   ASP A 358 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   ASN B 359 " --> pdb=" O   ASP A 358 " (cutoff:3.500A)
      removed outlier: 8.909A  pdb=" N   GLY A 355 " --> pdb=" O   SER D 356 " (cutoff:3.500A)
      removed outlier: 10.094A  pdb=" N   ASP D 358 " --> pdb=" O   GLY A 355 " (cutoff:3.500A)
      removed outlier: 8.835A  pdb=" N   LEU A 357 " --> pdb=" O   ASP D 358 " (cutoff:3.500A)
      removed outlier: 9.226A  pdb=" N   ILE D 360 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   ASN A 359 " --> pdb=" O   ILE D 360 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   HIS D 362 " --> pdb=" O   ASN A 359 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   THR A 361 " --> pdb=" O   HIS D 362 " (cutoff:3.500A)
      removed outlier: 8.917A  pdb=" N   GLY D 355 " --> pdb=" O   SER E 356 " (cutoff:3.500A)
      removed outlier: 10.099A  pdb=" N   ASP E 358 " --> pdb=" O   GLY D 355 " (cutoff:3.500A)
      removed outlier: 8.844A  pdb=" N   LEU D 357 " --> pdb=" O   ASP E 358 " (cutoff:3.500A)
      removed outlier: 9.227A  pdb=" N   ILE E 360 " --> pdb=" O   LEU D 357 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   ASN D 359 " --> pdb=" O   ILE E 360 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   HIS E 362 " --> pdb=" O   ASN D 359 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   THR D 361 " --> pdb=" O   HIS E 362 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 369 through 373
      removed outlier: 6.932A  pdb=" N   LYS B 370 " --> pdb=" O   LYS C 369 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   LYS A 370 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   LYS A 369 " --> pdb=" O   LYS D 370 " (cutoff:3.500A)
      removed outlier: 8.627A  pdb=" N   GLU D 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   ILE A 371 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   LYS D 369 " --> pdb=" O   LYS E 370 " (cutoff:3.500A)
      removed outlier: 8.652A  pdb=" N   GLU E 372 " --> pdb=" O   LYS D 369 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   ILE D 371 " --> pdb=" O   GLU E 372 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 376 through 377
      removed outlier: 6.958A  pdb=" N   THR A 377 " --> pdb=" O   PHE D 378 " (cutoff:3.500A)

    80 hydrogen bonds defined for protein.
    240 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: 1.21

  Time building geometry restraints manager: 1.06 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1355
        1.34 -     1.46: 632
        1.46 -     1.58: 2118
        1.58 -     1.69: 0
        1.69 -     1.81: 10
  Bond restraints: 4115
  Sorted by residual:
  bond pdb=" N   SER B 352 "
       pdb=" CA  SER B 352 "
    ideal  model  delta    sigma   weight residual
    1.455  1.491 -0.037 1.27e-02 6.20e+03 8.31e+00
  bond pdb=" N   SER A 352 "
       pdb=" CA  SER A 352 "
    ideal  model  delta    sigma   weight residual
    1.455  1.491 -0.036 1.27e-02 6.20e+03 8.15e+00
  bond pdb=" N   SER D 352 "
       pdb=" CA  SER D 352 "
    ideal  model  delta    sigma   weight residual
    1.455  1.491 -0.036 1.27e-02 6.20e+03 8.13e+00
  bond pdb=" N   SER E 352 "
       pdb=" CA  SER E 352 "
    ideal  model  delta    sigma   weight residual
    1.455  1.491 -0.036 1.27e-02 6.20e+03 8.13e+00
  bond pdb=" N   SER C 352 "
       pdb=" CA  SER C 352 "
    ideal  model  delta    sigma   weight residual
    1.455  1.491 -0.036 1.27e-02 6.20e+03 8.07e+00
  ... (remaining 4110 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.92: 4961
        0.92 -     1.84: 344
        1.84 -     2.77: 120
        2.77 -     3.69: 55
        3.69 -     4.61: 15
  Bond angle restraints: 5495
  Sorted by residual:
  angle pdb=" N   GLN A 351 "
        pdb=" CA  GLN A 351 "
        pdb=" C   GLN A 351 "
      ideal   model   delta    sigma   weight residual
     112.30  107.69    4.61 1.36e+00 5.41e-01 1.15e+01
  angle pdb=" N   GLN C 351 "
        pdb=" CA  GLN C 351 "
        pdb=" C   GLN C 351 "
      ideal   model   delta    sigma   weight residual
     112.30  107.70    4.60 1.36e+00 5.41e-01 1.14e+01
  angle pdb=" N   GLN E 351 "
        pdb=" CA  GLN E 351 "
        pdb=" C   GLN E 351 "
      ideal   model   delta    sigma   weight residual
     112.30  107.70    4.60 1.36e+00 5.41e-01 1.14e+01
  angle pdb=" N   GLN B 351 "
        pdb=" CA  GLN B 351 "
        pdb=" C   GLN B 351 "
      ideal   model   delta    sigma   weight residual
     112.30  107.72    4.58 1.36e+00 5.41e-01 1.13e+01
  angle pdb=" N   GLN D 351 "
        pdb=" CA  GLN D 351 "
        pdb=" C   GLN D 351 "
      ideal   model   delta    sigma   weight residual
     112.30  107.72    4.58 1.36e+00 5.41e-01 1.13e+01
  ... (remaining 5490 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.40: 2160
       11.40 -    22.79: 235
       22.79 -    34.18: 95
       34.18 -    45.58: 20
       45.58 -    56.97: 15
  Dihedral angle restraints: 2525
    sinusoidal: 1055
      harmonic: 1470
  Sorted by residual:
  dihedral pdb=" CA  ASP D 358 "
           pdb=" CB  ASP D 358 "
           pdb=" CG  ASP D 358 "
           pdb=" OD1 ASP D 358 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -82.26   52.26     1      2.00e+01 2.50e-03 9.31e+00
  dihedral pdb=" CA  ASP E 358 "
           pdb=" CB  ASP E 358 "
           pdb=" CG  ASP E 358 "
           pdb=" OD1 ASP E 358 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -82.23   52.23     1      2.00e+01 2.50e-03 9.30e+00
  dihedral pdb=" CA  ASP A 358 "
           pdb=" CB  ASP A 358 "
           pdb=" CG  ASP A 358 "
           pdb=" OD1 ASP A 358 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -82.22   52.22     1      2.00e+01 2.50e-03 9.30e+00
  ... (remaining 2522 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 417
       0.041 -    0.082: 83
       0.082 -    0.122: 91
       0.122 -    0.163: 9
       0.163 -    0.204: 15
  Chirality restraints: 615
  Sorted by residual:
  chirality pdb=" CB  ILE C 360 "
            pdb=" CA  ILE C 360 "
            pdb=" CG1 ILE C 360 "
            pdb=" CG2 ILE C 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CB  ILE E 360 "
            pdb=" CA  ILE E 360 "
            pdb=" CG1 ILE E 360 "
            pdb=" CG2 ILE E 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CB  ILE D 360 "
            pdb=" CA  ILE D 360 "
            pdb=" CG1 ILE D 360 "
            pdb=" CG2 ILE D 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 612 not shown)

  Planarity restraints: 705
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG C 349 "    0.010 2.00e-02 2.50e+03   2.03e-02 4.11e+00
        pdb=" C   ARG C 349 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   ARG C 349 "    0.013 2.00e-02 2.50e+03
        pdb=" N   VAL C 350 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 349 "    0.010 2.00e-02 2.50e+03   2.00e-02 4.00e+00
        pdb=" C   ARG A 349 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   ARG A 349 "    0.013 2.00e-02 2.50e+03
        pdb=" N   VAL A 350 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG D 349 "    0.010 2.00e-02 2.50e+03   1.99e-02 3.97e+00
        pdb=" C   ARG D 349 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   ARG D 349 "    0.013 2.00e-02 2.50e+03
        pdb=" N   VAL D 350 "    0.012 2.00e-02 2.50e+03
  ... (remaining 702 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 1398
        2.89 -     3.39: 3508
        3.39 -     3.90: 6963
        3.90 -     4.40: 7450
        4.40 -     4.90: 15049
  Nonbonded interactions: 34368
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 289 "
            pdb=" OG  SER C 320 "
     model   vdw
     2.388 3.040
  nonbonded pdb=" OG  SER A 289 "
            pdb=" OG  SER A 320 "
     model   vdw
     2.389 3.040
  nonbonded pdb=" OG  SER D 289 "
            pdb=" OG  SER D 320 "
     model   vdw
     2.389 3.040
  nonbonded pdb=" OG  SER B 289 "
            pdb=" OG  SER B 320 "
     model   vdw
     2.389 3.040
  nonbonded pdb=" OG  SER E 289 "
            pdb=" OG  SER E 320 "
     model   vdw
     2.389 3.040
  ... (remaining 34363 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

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:             2.840
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     14.160
  Find NCS groups from input model:        0.070
  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:13.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
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      :  0.004   0.037   4115  Z= 0.238
  Angle     :  0.661   4.610   5495  Z= 0.423
  Chirality :  0.059   0.204    615
  Planarity :  0.004   0.020    705
  Dihedral  : 12.126  56.974   1595
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  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: -2.50 (0.29), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.90 (0.22), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 330 
 PHE   0.014   0.002   PHE E 346 
 TYR   0.004   0.001   TYR A 310 
 ARG   0.002   0.001   ARG E 349 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.465 
Fit side-chains
REVERT: A  372 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7381 (mm-30)
REVERT: B  310 TYR cc_start: 0.7964 (t80) cc_final: 0.7753 (t80)
REVERT: B  372 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7579 (mm-30)
REVERT: D  315 LEU cc_start: 0.9184 (mp) cc_final: 0.8967 (mt)
REVERT: D  372 GLU cc_start: 0.7459 (mm-30) cc_final: 0.6859 (mm-30)
REVERT: E  372 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7062 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.8026
  time to fit residues: 91.7436
Evaluate side-chains
  84 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 37 optimal weight:    8.9990
   chunk 21 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 25 optimal weight:    8.9990
   chunk 20 optimal weight:    0.0770
   chunk 39 optimal weight:    8.9990
   chunk 15 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 29 optimal weight:    7.9990
   chunk 45 optimal weight:    7.9990
   overall best weight:    3.5944

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

Flipped N/Q/H residues before XYZ refinement:
A 296 ASN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 374 HIS
B 288 GLN
B 296 ASN
B 351 GLN
** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 374 HIS
C 296 ASN
C 351 GLN
C 374 HIS
D 296 ASN
D 351 GLN
D 374 HIS
E 288 GLN
E 296 ASN
** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 351 GLN
E 368 ASN
E 374 HIS

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.099069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.087488 restraints weight = 6274.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 2.27
r_work: 0.3314 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3198 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.3006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.046   4115  Z= 0.493
  Angle     :  0.666   7.380   5495  Z= 0.341
  Chirality :  0.052   0.143    615
  Planarity :  0.004   0.032    705
  Dihedral  :  5.418  18.989    550
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  :  9.68 %
    Favored  : 86.02 %
  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: -2.51 (0.29), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.90 (0.22), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS C 362 
 PHE   0.021   0.004   PHE D 346 
 TYR   0.012   0.002   TYR D 310 
 ARG   0.003   0.001   ARG C 349 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.470 
Fit side-chains
REVERT: A  274 LYS cc_start: 0.7725 (mtmt) cc_final: 0.7267 (mtpp)
REVERT: A  315 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8800 (mt)
REVERT: A  345 ASP cc_start: 0.7161 (m-30) cc_final: 0.6935 (m-30)
REVERT: A  358 ASP cc_start: 0.8497 (p0) cc_final: 0.8231 (p0)
REVERT: B  274 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7844 (ptmt)
REVERT: B  305 SER cc_start: 0.9186 (p) cc_final: 0.8952 (p)
REVERT: C  345 ASP cc_start: 0.7401 (m-30) cc_final: 0.7088 (m-30)
REVERT: C  352 SER cc_start: 0.7993 (t) cc_final: 0.7780 (m)
REVERT: C  379 ARG cc_start: 0.7128 (tpt-90) cc_final: 0.6338 (mmp-170)
REVERT: D  274 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7899 (ptmt)
REVERT: D  288 GLN cc_start: 0.8936 (mt0) cc_final: 0.8659 (mt0)
REVERT: D  315 LEU cc_start: 0.9078 (mp) cc_final: 0.8841 (mt)
REVERT: D  345 ASP cc_start: 0.7086 (m-30) cc_final: 0.6591 (m-30)
REVERT: E  274 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7806 (ptmt)
REVERT: E  276 GLN cc_start: 0.8174 (mt0) cc_final: 0.7944 (mt0)
REVERT: E  379 ARG cc_start: 0.7358 (tpt-90) cc_final: 0.5958 (pmt170)
  outliers start: 20
  outliers final: 5
  residues processed: 99
  average time/residue: 0.9993
  time to fit residues: 103.0108
Evaluate side-chains
  91 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue  274 LYS
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain D residue  274 LYS
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain E residue  274 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   chunk 27 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 288 GLN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 276 GLN
B 288 GLN
** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 279 ASN
** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 288 GLN
** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.098812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.087130 restraints weight = 6318.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 2.28
r_work: 0.3301 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3186 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.3407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   4115  Z= 0.403
  Angle     :  0.608   5.714   5495  Z= 0.313
  Chirality :  0.051   0.147    615
  Planarity :  0.004   0.035    705
  Dihedral  :  5.155  16.012    550
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 15.70 %
    Favored  : 81.51 %
  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: -2.67 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.03 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 330 
 PHE   0.019   0.004   PHE E 346 
 TYR   0.012   0.002   TYR E 310 
 ARG   0.002   0.000   ARG E 349 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.558 
Fit side-chains
REVERT: A  315 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8854 (mt)
REVERT: A  345 ASP cc_start: 0.7179 (m-30) cc_final: 0.6945 (m-30)
REVERT: A  358 ASP cc_start: 0.8520 (p0) cc_final: 0.8301 (p0)
REVERT: B  310 TYR cc_start: 0.8839 (t80) cc_final: 0.8605 (t80)
REVERT: B  379 ARG cc_start: 0.6741 (tpt-90) cc_final: 0.6357 (tmt170)
REVERT: C  379 ARG cc_start: 0.7260 (tpt-90) cc_final: 0.6611 (mmp-170)
REVERT: D  288 GLN cc_start: 0.8915 (mt0) cc_final: 0.8693 (mt0)
REVERT: D  345 ASP cc_start: 0.7113 (m-30) cc_final: 0.6661 (m-30)
REVERT: E  372 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8080 (mp0)
REVERT: E  379 ARG cc_start: 0.7032 (tpt-90) cc_final: 0.6456 (pmt170)
  outliers start: 13
  outliers final: 5
  residues processed: 86
  average time/residue: 0.8938
  time to fit residues: 80.4381
Evaluate side-chains
  82 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain E residue  372 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 5 optimal weight:    8.9990
   chunk 7 optimal weight:    7.9990
   chunk 33 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 288 GLN
** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 276 GLN
C 307 GLN
D 276 GLN
** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 288 GLN
** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 368 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.101415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.090082 restraints weight = 6331.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 2.24
r_work: 0.3367 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.3447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4115  Z= 0.186
  Angle     :  0.513   7.073   5495  Z= 0.261
  Chirality :  0.049   0.143    615
  Planarity :  0.003   0.030    705
  Dihedral  :  4.788  16.223    550
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 15.48 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.71 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.06 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C 362 
 PHE   0.018   0.003   PHE D 346 
 TYR   0.008   0.001   TYR D 310 
 ARG   0.001   0.000   ARG E 349 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.523 
Fit side-chains
REVERT: A  315 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8843 (mt)
REVERT: A  345 ASP cc_start: 0.7129 (m-30) cc_final: 0.6891 (m-30)
REVERT: A  358 ASP cc_start: 0.8433 (p0) cc_final: 0.8208 (p0)
REVERT: A  379 ARG cc_start: 0.7109 (tmt-80) cc_final: 0.6648 (tmt170)
REVERT: B  379 ARG cc_start: 0.6691 (tpt-90) cc_final: 0.6217 (tmt-80)
REVERT: C  356 SER cc_start: 0.8565 (t) cc_final: 0.8363 (t)
REVERT: C  379 ARG cc_start: 0.7246 (tpt-90) cc_final: 0.6541 (mmp-170)
REVERT: D  288 GLN cc_start: 0.8867 (mt0) cc_final: 0.8585 (mt0)
REVERT: D  315 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8731 (mt)
REVERT: D  345 ASP cc_start: 0.6986 (m-30) cc_final: 0.6547 (m-30)
REVERT: E  372 GLU cc_start: 0.8475 (mp0) cc_final: 0.8154 (mp0)
REVERT: E  379 ARG cc_start: 0.6865 (tpt-90) cc_final: 0.6286 (pmt-80)
  outliers start: 13
  outliers final: 3
  residues processed: 85
  average time/residue: 0.8537
  time to fit residues: 76.2752
Evaluate side-chains
  82 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  360 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 35 optimal weight:   10.0000
   chunk 30 optimal weight:    7.9990
   chunk 42 optimal weight:    5.9990
   chunk 39 optimal weight:    9.9990
   chunk 9 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   chunk 19 optimal weight:    6.9990
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 36 optimal weight:    8.9990
   overall best weight:    1.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 288 GLN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 276 GLN
C 279 ASN
C 288 GLN
D 276 GLN
** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 288 GLN
** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.099950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.088442 restraints weight = 6495.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 2.33
r_work: 0.3333 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3217 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.3587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4115  Z= 0.278
  Angle     :  0.548   6.840   5495  Z= 0.278
  Chirality :  0.050   0.145    615
  Planarity :  0.003   0.032    705
  Dihedral  :  4.875  16.467    550
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 16.34 %
    Favored  : 80.65 %
  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: -2.76 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.09 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 362 
 PHE   0.018   0.003   PHE D 346 
 TYR   0.011   0.002   TYR C 310 
 ARG   0.002   0.000   ARG E 349 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.522 
Fit side-chains
REVERT: A  315 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8865 (mt)
REVERT: A  345 ASP cc_start: 0.7181 (m-30) cc_final: 0.6949 (m-30)
REVERT: A  349 ARG cc_start: 0.7968 (tpt-90) cc_final: 0.7757 (tpt-90)
REVERT: A  358 ASP cc_start: 0.8456 (p0) cc_final: 0.8238 (p0)
REVERT: A  379 ARG cc_start: 0.7054 (tmt-80) cc_final: 0.6531 (tmt-80)
REVERT: B  379 ARG cc_start: 0.6669 (tpt-90) cc_final: 0.6363 (tmt-80)
REVERT: C  276 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8142 (mp10)
REVERT: C  356 SER cc_start: 0.8627 (t) cc_final: 0.8411 (t)
REVERT: C  379 ARG cc_start: 0.7272 (tpt-90) cc_final: 0.6586 (mmp-170)
REVERT: D  288 GLN cc_start: 0.8872 (mt0) cc_final: 0.8620 (mt0)
REVERT: D  315 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8566 (mp)
REVERT: D  345 ASP cc_start: 0.7041 (m-30) cc_final: 0.6659 (m-30)
REVERT: E  372 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8220 (mp0)
REVERT: E  379 ARG cc_start: 0.6924 (tpt-90) cc_final: 0.6439 (pmt-80)
  outliers start: 14
  outliers final: 7
  residues processed: 83
  average time/residue: 0.8947
  time to fit residues: 77.7277
Evaluate side-chains
  88 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain C residue  276 GLN
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain E residue  372 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 45 optimal weight:    7.9990
   chunk 4 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 6 optimal weight:    9.9990
   chunk 11 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9990
   chunk 8 optimal weight:    7.9990
   chunk 13 optimal weight:    0.7980
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 276 GLN
C 288 GLN
D 276 GLN
** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 288 GLN
** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.101487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.090193 restraints weight = 6261.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 2.28
r_work: 0.3374 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3256 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.3583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4115  Z= 0.192
  Angle     :  0.521   6.766   5495  Z= 0.264
  Chirality :  0.049   0.142    615
  Planarity :  0.003   0.030    705
  Dihedral  :  4.730  15.810    550
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 16.34 %
    Favored  : 80.43 %
  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: -2.75 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.08 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C 362 
 PHE   0.017   0.002   PHE D 346 
 TYR   0.010   0.001   TYR C 310 
 ARG   0.001   0.000   ARG E 349 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.478 
Fit side-chains
REVERT: A  315 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8883 (mt)
REVERT: A  345 ASP cc_start: 0.7170 (m-30) cc_final: 0.6942 (m-30)
REVERT: A  349 ARG cc_start: 0.7967 (tpt-90) cc_final: 0.7747 (tpt-90)
REVERT: A  358 ASP cc_start: 0.8407 (p0) cc_final: 0.8182 (p0)
REVERT: A  379 ARG cc_start: 0.7041 (tmt-80) cc_final: 0.6356 (tmt-80)
REVERT: B  379 ARG cc_start: 0.6624 (tpt-90) cc_final: 0.6346 (tmt-80)
REVERT: C  276 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8245 (mp10)
REVERT: C  356 SER cc_start: 0.8653 (t) cc_final: 0.8427 (t)
REVERT: C  379 ARG cc_start: 0.7262 (tpt-90) cc_final: 0.6572 (mmp-170)
REVERT: D  288 GLN cc_start: 0.8878 (mt0) cc_final: 0.8641 (mt0)
REVERT: D  315 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8703 (mt)
REVERT: D  345 ASP cc_start: 0.7031 (m-30) cc_final: 0.6659 (m-30)
REVERT: E  372 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8196 (mp0)
REVERT: E  379 ARG cc_start: 0.6708 (tpt-90) cc_final: 0.6358 (pmt-80)
  outliers start: 15
  outliers final: 7
  residues processed: 81
  average time/residue: 0.9283
  time to fit residues: 78.4733
Evaluate side-chains
  87 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain C residue  276 GLN
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  372 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:    6.9990
   chunk 47 optimal weight:    8.9990
   chunk 11 optimal weight:    7.9990
   chunk 29 optimal weight:    7.9990
   chunk 5 optimal weight:    8.9990
   chunk 30 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   overall best weight:    3.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 288 GLN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 276 GLN
C 288 GLN
D 276 GLN
** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 288 GLN
** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.097680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.086025 restraints weight = 6467.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 2.31
r_work: 0.3291 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3175 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.3821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050   4115  Z= 0.494
  Angle     :  0.637   6.685   5495  Z= 0.329
  Chirality :  0.053   0.156    615
  Planarity :  0.004   0.037    705
  Dihedral  :  5.132  16.814    550
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 16.34 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.91 (0.27), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.21 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS A 330 
 PHE   0.019   0.003   PHE D 346 
 TYR   0.013   0.003   TYR C 310 
 ARG   0.003   0.001   ARG E 349 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.519 
Fit side-chains
REVERT: A  315 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8853 (mt)
REVERT: A  345 ASP cc_start: 0.7269 (m-30) cc_final: 0.6929 (m-30)
REVERT: A  358 ASP cc_start: 0.8529 (p0) cc_final: 0.8310 (p0)
REVERT: A  379 ARG cc_start: 0.7114 (tmt-80) cc_final: 0.6519 (tmt-80)
REVERT: B  379 ARG cc_start: 0.6920 (tpt-90) cc_final: 0.6597 (tmt-80)
REVERT: C  276 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8033 (mp10)
REVERT: C  379 ARG cc_start: 0.7315 (tpt-90) cc_final: 0.6434 (tpm170)
REVERT: D  288 GLN cc_start: 0.8882 (mt0) cc_final: 0.8591 (mt0)
REVERT: D  315 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8583 (mp)
REVERT: D  345 ASP cc_start: 0.7193 (m-30) cc_final: 0.6989 (m-30)
REVERT: E  372 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8293 (mp0)
REVERT: E  379 ARG cc_start: 0.7030 (tpt-90) cc_final: 0.6423 (pmt-80)
  outliers start: 17
  outliers final: 8
  residues processed: 85
  average time/residue: 0.9230
  time to fit residues: 82.1727
Evaluate side-chains
  89 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain C residue  276 GLN
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  372 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 48 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9980
   chunk 45 optimal weight:    6.9990
   chunk 41 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 13 optimal weight:    0.5980
   chunk 19 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 276 GLN
D 276 GLN
E 276 GLN
E 288 GLN
** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.099787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.088372 restraints weight = 6259.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 2.28
r_work: 0.3340 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3223 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.3802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4115  Z= 0.249
  Angle     :  0.550   6.970   5495  Z= 0.280
  Chirality :  0.050   0.144    615
  Planarity :  0.003   0.034    705
  Dihedral  :  4.929  16.321    550
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 18.06 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.88 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.18 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 362 
 PHE   0.018   0.003   PHE D 346 
 TYR   0.012   0.002   TYR B 310 
 ARG   0.001   0.000   ARG E 349 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.492 
Fit side-chains
REVERT: A  315 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8881 (mt)
REVERT: A  358 ASP cc_start: 0.8484 (p0) cc_final: 0.8253 (p0)
REVERT: A  379 ARG cc_start: 0.6968 (tmt-80) cc_final: 0.6398 (tmt-80)
REVERT: B  379 ARG cc_start: 0.6755 (tpt-90) cc_final: 0.6428 (tmt-80)
REVERT: C  276 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8276 (mp10)
REVERT: C  379 ARG cc_start: 0.7258 (tpt-90) cc_final: 0.6402 (tpm170)
REVERT: D  288 GLN cc_start: 0.8837 (mt0) cc_final: 0.8580 (mt0)
REVERT: D  315 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8600 (mp)
REVERT: E  372 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8148 (mp0)
REVERT: E  379 ARG cc_start: 0.6788 (tpt-90) cc_final: 0.6412 (pmt-80)
  outliers start: 13
  outliers final: 7
  residues processed: 78
  average time/residue: 0.8344
  time to fit residues: 68.3773
Evaluate side-chains
  87 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain C residue  276 GLN
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  372 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 18 optimal weight:    6.9990
   chunk 4 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 49 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 276 GLN
C 279 ASN
D 276 GLN
** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 288 GLN
** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.099541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.088076 restraints weight = 6261.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3460 rms_B_bonded: 2.28
r_work: 0.3334 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3217 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.3814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4115  Z= 0.283
  Angle     :  0.561   6.907   5495  Z= 0.285
  Chirality :  0.050   0.145    615
  Planarity :  0.003   0.034    705
  Dihedral  :  4.912  16.333    550
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 17.85 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.91 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.21 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 362 
 PHE   0.019   0.003   PHE D 346 
 TYR   0.012   0.002   TYR B 310 
 ARG   0.001   0.000   ARG E 349 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.480 
Fit side-chains
REVERT: A  315 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8881 (mt)
REVERT: A  358 ASP cc_start: 0.8529 (p0) cc_final: 0.8308 (p0)
REVERT: A  379 ARG cc_start: 0.6994 (tmt-80) cc_final: 0.6430 (tmt-80)
REVERT: B  379 ARG cc_start: 0.6811 (tpt-90) cc_final: 0.6540 (tmt-80)
REVERT: C  276 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8284 (mp10)
REVERT: C  379 ARG cc_start: 0.7206 (tpt-90) cc_final: 0.6433 (tpm170)
REVERT: D  288 GLN cc_start: 0.8860 (mt0) cc_final: 0.8603 (mt0)
REVERT: D  315 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8593 (mp)
REVERT: E  372 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8200 (mp0)
REVERT: E  379 ARG cc_start: 0.6807 (tpt-90) cc_final: 0.6433 (pmt-80)
  outliers start: 14
  outliers final: 8
  residues processed: 83
  average time/residue: 0.8562
  time to fit residues: 74.5147
Evaluate side-chains
  88 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain C residue  276 GLN
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  372 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   chunk 19 optimal weight:    7.9990
   chunk 49 optimal weight:    0.7980
   chunk 39 optimal weight:    0.5980
   chunk 25 optimal weight:    6.9990
   chunk 15 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 7 optimal weight:   10.0000
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 276 GLN
D 276 GLN
E 276 GLN
E 288 GLN
** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.100755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.089312 restraints weight = 6196.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 2.27
r_work: 0.3362 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.3840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4115  Z= 0.221
  Angle     :  0.543   6.780   5495  Z= 0.276
  Chirality :  0.050   0.143    615
  Planarity :  0.003   0.033    705
  Dihedral  :  4.824  15.974    550
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 19.14 %
    Favored  : 78.28 %
  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: -2.89 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.19 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 362 
 PHE   0.018   0.003   PHE D 346 
 TYR   0.014   0.002   TYR B 310 
 ARG   0.001   0.000   ARG E 349 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.470 
Fit side-chains
REVERT: A  315 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8880 (mt)
REVERT: A  349 ARG cc_start: 0.8075 (ttt180) cc_final: 0.7757 (tpt-90)
REVERT: A  358 ASP cc_start: 0.8510 (p0) cc_final: 0.8262 (p0)
REVERT: A  379 ARG cc_start: 0.6991 (tmt-80) cc_final: 0.6423 (tmt-80)
REVERT: B  379 ARG cc_start: 0.6774 (tpt-90) cc_final: 0.6510 (tmt-80)
REVERT: C  276 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8253 (mp10)
REVERT: C  379 ARG cc_start: 0.7201 (tpt-90) cc_final: 0.6386 (tpm170)
REVERT: D  288 GLN cc_start: 0.8861 (mt0) cc_final: 0.8618 (mt0)
REVERT: D  315 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8643 (mp)
REVERT: E  372 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8197 (mp0)
REVERT: E  379 ARG cc_start: 0.6804 (tpt-90) cc_final: 0.6441 (pmt-80)
  outliers start: 12
  outliers final: 8
  residues processed: 80
  average time/residue: 0.8304
  time to fit residues: 69.9972
Evaluate side-chains
  88 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain C residue  276 GLN
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  372 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 34 optimal weight:    0.7980
   chunk 43 optimal weight:    0.3980
   chunk 3 optimal weight:    0.7980
   chunk 29 optimal weight:    6.9990
   chunk 17 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 26 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0020
   overall best weight:    1.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 276 GLN
C 279 ASN
D 276 GLN
E 276 GLN
E 288 GLN
** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.101446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.090102 restraints weight = 6243.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 2.30
r_work: 0.3366 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3247 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.3815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4115  Z= 0.197
  Angle     :  0.540   7.093   5495  Z= 0.274
  Chirality :  0.049   0.141    615
  Planarity :  0.003   0.032    705
  Dihedral  :  4.744  15.612    550
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 19.78 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.88 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.19 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 362 
 PHE   0.018   0.003   PHE D 346 
 TYR   0.015   0.002   TYR B 310 
 ARG   0.001   0.000   ARG D 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3079.41 seconds
wall clock time: 55 minutes 26.40 seconds (3326.40 seconds total)