Starting phenix.real_space_refine
on Tue Mar  3 12:19:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p66_13219/03_2026/7p66_13219.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p66_13219/03_2026/7p66_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p66_13219/03_2026/7p66_13219.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p66_13219/03_2026/7p66_13219.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p66_13219/03_2026/7p66_13219.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p66_13219/03_2026/7p66_13219.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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:
    B, C, D, E
  Time building chain proxies: 0.55, per 1000 atoms: 0.14
  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: 0.20
  Conformation dependent library (CDL) restraints added in 153.6 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: 0.21
  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: 0.48

  Time building geometry restraints manager: 0.32 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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:             2.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.750
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.000
  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:7.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.750
-------------------------------------------------------------------------------
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= 0.251
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.002   0.001   ARG E 349 
 TYR   0.004   0.001   TYR A 310 
 PHE   0.014   0.002   PHE E 346 
 HIS   0.002   0.001   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 4115)
  covalent geometry    : angle       0.66078 ( 5495)
  hydrogen bonds       : bond        0.13826 (   80)
  hydrogen bonds       : angle       7.63311 (  240)

*********************** 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  : 0.113 
Fit side-chains
REVERT: A  372 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7384 (mm-30)
REVERT: B  310 TYR cc_start: 0.7966 (t80) cc_final: 0.7753 (t80)
REVERT: B  372 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7579 (mm-30)
REVERT: D  315 LEU cc_start: 0.9184 (mp) cc_final: 0.8968 (mt)
REVERT: D  372 GLU cc_start: 0.7455 (mm-30) cc_final: 0.6849 (mm-30)
REVERT: E  372 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7063 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.3724
  time to fit residues: 42.3337
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  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    7.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 19 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
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 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3600 r_free = 0.3600 target = 0.099207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.087618 restraints weight = 6355.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 2.30
r_work: 0.3313 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.3010

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= 0.311
  Angle     :  0.663   7.052   5495  Z= 0.339
  Chirality :  0.052   0.142    615
  Planarity :  0.004   0.032    705
  Dihedral  :  5.345  18.632    550
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 10.32 %
    Favored  : 85.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.002   0.001   ARG A 349 
 TYR   0.012   0.002   TYR D 310 
 PHE   0.022   0.004   PHE D 346 
 HIS   0.004   0.001   HIS C 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00721 ( 4115)
  covalent geometry    : angle       0.66255 ( 5495)
  hydrogen bonds       : bond        0.02553 (   80)
  hydrogen bonds       : angle       5.07613 (  240)

*********************** 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
  109 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A  274 LYS cc_start: 0.7698 (mtmt) cc_final: 0.7054 (mttm)
REVERT: A  315 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8798 (mt)
REVERT: A  345 ASP cc_start: 0.7159 (m-30) cc_final: 0.6926 (m-30)
REVERT: A  358 ASP cc_start: 0.8491 (p0) cc_final: 0.8227 (p0)
REVERT: B  274 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7887 (ptmt)
REVERT: B  310 TYR cc_start: 0.8827 (t80) cc_final: 0.8588 (t80)
REVERT: C  345 ASP cc_start: 0.7391 (m-30) cc_final: 0.7077 (m-30)
REVERT: C  379 ARG cc_start: 0.7118 (tpt-90) cc_final: 0.6376 (mmp-170)
REVERT: D  274 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7838 (ptmt)
REVERT: D  288 GLN cc_start: 0.8939 (mt0) cc_final: 0.8596 (mt0)
REVERT: D  315 LEU cc_start: 0.9102 (mp) cc_final: 0.8853 (mt)
REVERT: D  345 ASP cc_start: 0.7083 (m-30) cc_final: 0.6593 (m-30)
REVERT: E  274 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7843 (ptmt)
REVERT: E  276 GLN cc_start: 0.8144 (mt0) cc_final: 0.7887 (mt0)
REVERT: E  379 ARG cc_start: 0.7360 (tpt-90) cc_final: 0.5952 (pmt170)
  outliers start: 20
  outliers final: 5
  residues processed: 98
  average time/residue: 0.4358
  time to fit residues: 44.2353
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  : 0.137 
-------------------------------------------------------------------------------
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 18 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0040
   chunk 2 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 22 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0050
   overall best weight:    1.1610

-------------------------------------------------------------------------------
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 276 GLN
C 279 ASN
C 307 GLN
E 288 GLN
** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.102048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.090495 restraints weight = 6288.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 2.29
r_work: 0.3369 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3255 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.3076

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= 0.124
  Angle     :  0.526   5.786   5495  Z= 0.267
  Chirality :  0.050   0.144    615
  Planarity :  0.003   0.029    705
  Dihedral  :  4.763  15.759    550
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 14.62 %
    Favored  : 83.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.58 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.96 (0.22), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 349 
 TYR   0.007   0.001   TYR E 310 
 PHE   0.016   0.003   PHE E 346 
 HIS   0.003   0.001   HIS C 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4115)
  covalent geometry    : angle       0.52636 ( 5495)
  hydrogen bonds       : bond        0.02166 (   80)
  hydrogen bonds       : angle       4.59679 (  240)

*********************** 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
  93 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 0.109 
Fit side-chains
REVERT: A  274 LYS cc_start: 0.7735 (mtmt) cc_final: 0.7526 (mtpt)
REVERT: A  315 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8793 (mt)
REVERT: A  345 ASP cc_start: 0.7175 (m-30) cc_final: 0.6832 (m-30)
REVERT: A  358 ASP cc_start: 0.8458 (p0) cc_final: 0.8202 (p0)
REVERT: B  310 TYR cc_start: 0.8712 (t80) cc_final: 0.8461 (t80)
REVERT: B  338 GLU cc_start: 0.8412 (mt-10) cc_final: 0.7913 (tt0)
REVERT: B  379 ARG cc_start: 0.6393 (tpt-90) cc_final: 0.5871 (tmt-80)
REVERT: C  345 ASP cc_start: 0.7408 (m-30) cc_final: 0.7093 (m-30)
REVERT: C  379 ARG cc_start: 0.7030 (tpt-90) cc_final: 0.6331 (mmp-170)
REVERT: D  288 GLN cc_start: 0.8884 (mt0) cc_final: 0.8601 (mt0)
REVERT: D  345 ASP cc_start: 0.6931 (m-30) cc_final: 0.6400 (m-30)
REVERT: D  372 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8160 (mp0)
REVERT: E  372 GLU cc_start: 0.8405 (mp0) cc_final: 0.8093 (mp0)
REVERT: E  379 ARG cc_start: 0.6947 (tpt-90) cc_final: 0.6002 (ppt90)
  outliers start: 9
  outliers final: 3
  residues processed: 86
  average time/residue: 0.4552
  time to fit residues: 40.7462
Evaluate side-chains
  83 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
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  360 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 23 optimal weight:    0.2980
   chunk 29 optimal weight:    0.4980
   chunk 42 optimal weight:    6.9990
   chunk 7 optimal weight:    9.9990
   chunk 43 optimal weight:    2.9990
   chunk 21 optimal weight:    8.9990
   chunk 16 optimal weight:    6.9990
   chunk 38 optimal weight:    8.9990
   chunk 8 optimal weight:    0.9980
   chunk 46 optimal weight:    7.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    1.7584

-------------------------------------------------------------------------------
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 288 GLN
** 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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.100648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.089091 restraints weight = 6255.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 2.26
r_work: 0.3332 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.3299

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= 0.168
  Angle     :  0.538   7.421   5495  Z= 0.272
  Chirality :  0.050   0.142    615
  Planarity :  0.003   0.031    705
  Dihedral  :  4.808  15.504    550
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 14.84 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.65 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.01 (0.22), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 349 
 TYR   0.009   0.002   TYR A 310 
 PHE   0.017   0.003   PHE D 346 
 HIS   0.003   0.001   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 4115)
  covalent geometry    : angle       0.53779 ( 5495)
  hydrogen bonds       : bond        0.02023 (   80)
  hydrogen bonds       : angle       4.49291 (  240)

*********************** 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
  95 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A  315 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8898 (mt)
REVERT: A  345 ASP cc_start: 0.7162 (m-30) cc_final: 0.6910 (m-30)
REVERT: A  358 ASP cc_start: 0.8443 (p0) cc_final: 0.8214 (p0)
REVERT: B  310 TYR cc_start: 0.8745 (t80) cc_final: 0.8504 (t80)
REVERT: B  379 ARG cc_start: 0.6685 (tpt-90) cc_final: 0.6297 (tmt-80)
REVERT: C  379 ARG cc_start: 0.7254 (tpt-90) cc_final: 0.6626 (mmp-170)
REVERT: D  288 GLN cc_start: 0.8908 (mt0) cc_final: 0.8685 (mt0)
REVERT: D  315 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8698 (mt)
REVERT: D  345 ASP cc_start: 0.6985 (m-30) cc_final: 0.6471 (m-30)
REVERT: E  372 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8203 (mp0)
REVERT: E  379 ARG cc_start: 0.6946 (tpt-90) cc_final: 0.6344 (pmt170)
  outliers start: 16
  outliers final: 5
  residues processed: 83
  average time/residue: 0.4157
  time to fit residues: 35.9524
Evaluate side-chains
  83 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  360 ILE
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 36 optimal weight:    9.9990
   chunk 9 optimal weight:   10.0000
   chunk 42 optimal weight:    0.0060
   chunk 28 optimal weight:    0.0770
   chunk 10 optimal weight:    9.9990
   chunk 46 optimal weight:    4.9990
   chunk 2 optimal weight:    6.9990
   chunk 7 optimal weight:   10.0000
   chunk 27 optimal weight:    7.9990
   chunk 23 optimal weight:    1.9990
   chunk 21 optimal weight:    7.9990
   overall best weight:    2.8160

-------------------------------------------------------------------------------
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 = 0.3599 r_free = 0.3599 target = 0.098264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.086866 restraints weight = 6326.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 2.27
r_work: 0.3315 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.3613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   4115  Z= 0.250
  Angle     :  0.594   7.319   5495  Z= 0.301
  Chirality :  0.051   0.158    615
  Planarity :  0.004   0.035    705
  Dihedral  :  5.046  17.139    550
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 13.76 %
    Favored  : 82.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.75 (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
 ARG   0.003   0.000   ARG E 349 
 TYR   0.012   0.003   TYR C 310 
 PHE   0.019   0.003   PHE D 346 
 HIS   0.003   0.001   HIS A 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00573 ( 4115)
  covalent geometry    : angle       0.59354 ( 5495)
  hydrogen bonds       : bond        0.02221 (   80)
  hydrogen bonds       : angle       4.64369 (  240)

*********************** 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
  96 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.106 
Fit side-chains
REVERT: A  315 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8863 (mt)
REVERT: A  345 ASP cc_start: 0.7181 (m-30) cc_final: 0.6931 (m-30)
REVERT: A  358 ASP cc_start: 0.8504 (p0) cc_final: 0.8281 (p0)
REVERT: A  379 ARG cc_start: 0.7114 (ttp80) cc_final: 0.6863 (tmt170)
REVERT: B  310 TYR cc_start: 0.8804 (t80) cc_final: 0.8580 (t80)
REVERT: B  379 ARG cc_start: 0.6770 (tpt-90) cc_final: 0.6492 (tmt-80)
REVERT: C  356 SER cc_start: 0.8610 (t) cc_final: 0.8387 (t)
REVERT: C  379 ARG cc_start: 0.7296 (tpt-90) cc_final: 0.6421 (tpm170)
REVERT: D  274 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7422 (ttpt)
REVERT: D  288 GLN cc_start: 0.8873 (mt0) cc_final: 0.8603 (mt0)
REVERT: D  315 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8562 (mp)
REVERT: D  345 ASP cc_start: 0.7070 (m-30) cc_final: 0.6682 (m-30)
REVERT: E  372 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8220 (mp0)
REVERT: E  379 ARG cc_start: 0.6962 (tpt-90) cc_final: 0.6453 (pmt-80)
  outliers start: 18
  outliers final: 9
  residues processed: 84
  average time/residue: 0.3973
  time to fit residues: 34.8053
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  : 0.110 
-------------------------------------------------------------------------------
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  274 LYS
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 10 optimal weight:   10.0000
   chunk 33 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 39 optimal weight:    8.9990
   chunk 25 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 21 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 29 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   overall best weight:    2.1784

-------------------------------------------------------------------------------
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
** 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 = 0.3616 r_free = 0.3616 target = 0.099377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.087909 restraints weight = 6367.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 2.28
r_work: 0.3329 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.3651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   4115  Z= 0.200
  Angle     :  0.567   7.011   5495  Z= 0.287
  Chirality :  0.050   0.147    615
  Planarity :  0.004   0.035    705
  Dihedral  :  4.947  16.998    550
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 16.56 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.80 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.13 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 349 
 TYR   0.012   0.002   TYR C 310 
 PHE   0.019   0.003   PHE D 346 
 HIS   0.003   0.001   HIS A 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 4115)
  covalent geometry    : angle       0.56711 ( 5495)
  hydrogen bonds       : bond        0.02055 (   80)
  hydrogen bonds       : angle       4.55051 (  240)

*********************** 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  : 0.118 
Fit side-chains
REVERT: A  315 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8868 (mt)
REVERT: A  345 ASP cc_start: 0.7133 (m-30) cc_final: 0.6894 (m-30)
REVERT: A  358 ASP cc_start: 0.8495 (p0) cc_final: 0.8277 (p0)
REVERT: A  379 ARG cc_start: 0.7219 (ttp80) cc_final: 0.6929 (tmt170)
REVERT: B  310 TYR cc_start: 0.8794 (t80) cc_final: 0.8555 (t80)
REVERT: B  379 ARG cc_start: 0.6726 (tpt-90) cc_final: 0.6502 (tmt-80)
REVERT: C  276 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8356 (mp10)
REVERT: C  356 SER cc_start: 0.8643 (t) cc_final: 0.8424 (t)
REVERT: C  379 ARG cc_start: 0.7228 (tpt-90) cc_final: 0.6433 (tpm170)
REVERT: D  288 GLN cc_start: 0.8879 (mt0) cc_final: 0.8622 (mt0)
REVERT: D  315 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8575 (mp)
REVERT: D  345 ASP cc_start: 0.7094 (m-30) cc_final: 0.6718 (m-30)
REVERT: E  372 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8181 (mp0)
REVERT: E  379 ARG cc_start: 0.6904 (tpt-90) cc_final: 0.6463 (pmt-80)
  outliers start: 15
  outliers final: 7
  residues processed: 82
  average time/residue: 0.4019
  time to fit residues: 34.3207
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  : 0.182 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 35 optimal weight:   10.0000
   chunk 13 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:    5.9990
   chunk 19 optimal weight:    0.7980
   chunk 10 optimal weight:    4.9990
   chunk 46 optimal weight:    8.9990
   chunk 8 optimal weight:    0.0470
   chunk 45 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.1280

-------------------------------------------------------------------------------
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 279 ASN
C 288 GLN
D 276 GLN
E 276 GLN
E 288 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.101064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.089748 restraints weight = 6351.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 2.29
r_work: 0.3363 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3247 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.3651

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= 0.121
  Angle     :  0.527   6.789   5495  Z= 0.265
  Chirality :  0.049   0.143    615
  Planarity :  0.003   0.031    705
  Dihedral  :  4.754  16.291    550
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 17.85 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.76 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.10 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 349 
 TYR   0.011   0.002   TYR C 310 
 PHE   0.017   0.002   PHE D 346 
 HIS   0.003   0.001   HIS C 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 4115)
  covalent geometry    : angle       0.52727 ( 5495)
  hydrogen bonds       : bond        0.01865 (   80)
  hydrogen bonds       : angle       4.38517 (  240)

*********************** 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
  90 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A  315 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8874 (mt)
REVERT: A  358 ASP cc_start: 0.8464 (p0) cc_final: 0.8226 (p0)
REVERT: A  379 ARG cc_start: 0.7236 (ttp80) cc_final: 0.7034 (ttp80)
REVERT: B  379 ARG cc_start: 0.6641 (tpt-90) cc_final: 0.6384 (tmt-80)
REVERT: C  276 GLN cc_start: 0.8835 (mt0) cc_final: 0.8292 (mp10)
REVERT: C  356 SER cc_start: 0.8661 (t) cc_final: 0.8434 (t)
REVERT: C  379 ARG cc_start: 0.7198 (tpt-90) cc_final: 0.6413 (tpm170)
REVERT: D  288 GLN cc_start: 0.8871 (mt0) cc_final: 0.8566 (mt0)
REVERT: D  315 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8689 (mt)
REVERT: D  345 ASP cc_start: 0.7060 (m-30) cc_final: 0.6786 (m-30)
REVERT: E  372 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8219 (mp0)
REVERT: E  379 ARG cc_start: 0.6722 (tpt-90) cc_final: 0.6382 (pmt-80)
  outliers start: 13
  outliers final: 8
  residues processed: 80
  average time/residue: 0.3147
  time to fit residues: 26.3380
Evaluate side-chains
  84 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
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  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 15 optimal weight:    6.9990
   chunk 23 optimal weight:    5.9990
   chunk 10 optimal weight:    9.9990
   chunk 22 optimal weight:    4.9990
   chunk 35 optimal weight:    9.9990
   chunk 14 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 44 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 12 optimal weight:    4.9990
   chunk 48 optimal weight:    0.0370
   overall best weight:    1.5262

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

Flipped N/Q/H residues before XYZ refinement:
A 288 GLN
** 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
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 = 0.3642 r_free = 0.3642 target = 0.100980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.089721 restraints weight = 6265.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 2.27
r_work: 0.3362 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3247 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.3650

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= 0.148
  Angle     :  0.532   7.052   5495  Z= 0.268
  Chirality :  0.050   0.142    615
  Planarity :  0.003   0.032    705
  Dihedral  :  4.748  15.905    550
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 17.85 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.79 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.12 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 349 
 TYR   0.010   0.002   TYR A 310 
 PHE   0.017   0.003   PHE D 346 
 HIS   0.002   0.001   HIS E 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 4115)
  covalent geometry    : angle       0.53161 ( 5495)
  hydrogen bonds       : bond        0.01870 (   80)
  hydrogen bonds       : angle       4.39870 (  240)

*********************** 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
  94 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.161 
Fit side-chains
REVERT: A  315 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8890 (mt)
REVERT: A  358 ASP cc_start: 0.8463 (p0) cc_final: 0.8210 (p0)
REVERT: A  379 ARG cc_start: 0.7257 (ttp80) cc_final: 0.6954 (tmt170)
REVERT: B  310 TYR cc_start: 0.8734 (t80) cc_final: 0.8502 (t80)
REVERT: B  379 ARG cc_start: 0.6709 (tpt-90) cc_final: 0.6507 (tmt-80)
REVERT: C  276 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8351 (mp10)
REVERT: C  379 ARG cc_start: 0.7207 (tpt-90) cc_final: 0.6429 (tpm170)
REVERT: D  288 GLN cc_start: 0.8874 (mt0) cc_final: 0.8622 (mt0)
REVERT: D  315 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8597 (mp)
REVERT: E  372 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8208 (mp0)
REVERT: E  379 ARG cc_start: 0.6775 (tpt-90) cc_final: 0.6448 (pmt-80)
  outliers start: 16
  outliers final: 9
  residues processed: 81
  average time/residue: 0.3804
  time to fit residues: 32.1776
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  : 0.154 
-------------------------------------------------------------------------------
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  319 THR
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 46 optimal weight:    8.9990
   chunk 1 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 5 optimal weight:   10.0000
   chunk 38 optimal weight:    7.9990
   chunk 23 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 37 optimal weight:    8.9990
   chunk 27 optimal weight:    8.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    2.1788

-------------------------------------------------------------------------------
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 = 0.3622 r_free = 0.3622 target = 0.099709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.088273 restraints weight = 6434.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 2.31
r_work: 0.3339 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3221 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.3730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   4115  Z= 0.198
  Angle     :  0.562   7.087   5495  Z= 0.285
  Chirality :  0.050   0.144    615
  Planarity :  0.003   0.034    705
  Dihedral  :  4.854  16.114    550
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 18.49 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.82 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 349 
 TYR   0.015   0.002   TYR C 310 
 PHE   0.018   0.003   PHE D 346 
 HIS   0.003   0.001   HIS E 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 4115)
  covalent geometry    : angle       0.56215 ( 5495)
  hydrogen bonds       : bond        0.02014 (   80)
  hydrogen bonds       : angle       4.47724 (  240)

*********************** 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: 15
    poor density    : 78
  time to evaluate  : 0.102 
Fit side-chains
REVERT: A  315 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8882 (mt)
REVERT: A  345 ASP cc_start: 0.7226 (m-30) cc_final: 0.6870 (m-30)
REVERT: A  358 ASP cc_start: 0.8544 (p0) cc_final: 0.8296 (p0)
REVERT: A  379 ARG cc_start: 0.7321 (ttp80) cc_final: 0.7013 (tmt170)
REVERT: C  276 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8316 (mp10)
REVERT: C  379 ARG cc_start: 0.7244 (tpt-90) cc_final: 0.6407 (tpm170)
REVERT: D  274 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7496 (ttpt)
REVERT: D  288 GLN cc_start: 0.8869 (mt0) cc_final: 0.8598 (mt0)
REVERT: D  315 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8576 (mp)
REVERT: E  372 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8236 (mp0)
REVERT: E  379 ARG cc_start: 0.6808 (tpt-90) cc_final: 0.6436 (pmt-80)
  outliers start: 15
  outliers final: 9
  residues processed: 82
  average time/residue: 0.3695
  time to fit residues: 31.6390
Evaluate side-chains
  92 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
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  319 THR
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain D residue  274 LYS
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 46 optimal weight:    0.0870
   chunk 9 optimal weight:    9.9990
   chunk 16 optimal weight:    7.9990
   chunk 29 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   chunk 15 optimal weight:    8.9990
   chunk 7 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 48 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    3.0166

-------------------------------------------------------------------------------
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 288 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.102007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.091025 restraints weight = 6025.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 2.02
r_work: 0.3334 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.3881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   4115  Z= 0.266
  Angle     :  0.610   7.155   5495  Z= 0.312
  Chirality :  0.052   0.147    615
  Planarity :  0.004   0.036    705
  Dihedral  :  5.039  16.459    550
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 19.14 %
    Favored  : 77.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.92 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.22 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 379 
 TYR   0.015   0.003   TYR C 310 
 PHE   0.020   0.003   PHE D 346 
 HIS   0.004   0.001   HIS A 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00605 ( 4115)
  covalent geometry    : angle       0.61041 ( 5495)
  hydrogen bonds       : bond        0.02196 (   80)
  hydrogen bonds       : angle       4.62444 (  240)

********************** 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
  91 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.167 
Fit side-chains
REVERT: A  315 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8901 (mt)
REVERT: A  358 ASP cc_start: 0.8583 (p0) cc_final: 0.8359 (p0)
REVERT: A  379 ARG cc_start: 0.7271 (ttp80) cc_final: 0.7069 (tmt170)
REVERT: C  276 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8316 (mp10)
REVERT: C  379 ARG cc_start: 0.7301 (tpt-90) cc_final: 0.6520 (tpm170)
REVERT: D  288 GLN cc_start: 0.8914 (mt0) cc_final: 0.8658 (mt0)
REVERT: D  315 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8621 (mp)
REVERT: D  345 ASP cc_start: 0.8111 (t0) cc_final: 0.7828 (t70)
REVERT: E  372 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8226 (mp0)
REVERT: E  379 ARG cc_start: 0.6984 (tpt-90) cc_final: 0.6575 (pmt-80)
  outliers start: 14
  outliers final: 9
  residues processed: 81
  average time/residue: 0.3394
  time to fit residues: 28.8823
Evaluate side-chains
  90 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
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  319 THR
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 22 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 15 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 48 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    1.3984

-------------------------------------------------------------------------------
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
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 = 0.3666 r_free = 0.3666 target = 0.104685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.093387 restraints weight = 5988.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 2.16
r_work: 0.3370 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3257 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.3854

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= 0.142
  Angle     :  0.549   6.884   5495  Z= 0.279
  Chirality :  0.050   0.142    615
  Planarity :  0.003   0.033    705
  Dihedral  :  4.828  16.013    550
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 19.35 %
    Favored  : 77.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.90 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.20 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 379 
 TYR   0.014   0.002   TYR C 310 
 PHE   0.018   0.002   PHE D 346 
 HIS   0.003   0.001   HIS E 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 4115)
  covalent geometry    : angle       0.54904 ( 5495)
  hydrogen bonds       : bond        0.01875 (   80)
  hydrogen bonds       : angle       4.49300 (  240)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1431.87 seconds
wall clock time: 25 minutes 17.25 seconds (1517.25 seconds total)