Starting phenix.real_space_refine
on Tue Mar  3 12:24:06 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p65_13218/03_2026/7p65_13218.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p65_13218/03_2026/7p65_13218.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p65_13218/03_2026/7p65_13218.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p65_13218/03_2026/7p65_13218.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p65_13218/03_2026/7p65_13218.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p65_13218/03_2026/7p65_13218.cif"
  }
  resolution = 2.7
  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    2575      2.51       5
     N     775      2.21       5
     O     785      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: 4145
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 829
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 4, 'TRANS': 105}
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 0.64, per 1000 atoms: 0.15
  Number of scatterers: 4145
  At special positions: 0
  Unit cell: (67.85, 111.55, 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     785      8.00
     N     775      7.00
     C    2575      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: 0.30
  Conformation dependent library (CDL) restraints added in 126.6 milliseconds
  

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  950

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 42.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 275 through 280
      removed outlier: 6.541A  pdb=" N   GLN B 276 " --> pdb=" O   ILE C 277 " (cutoff:3.500A)
      removed outlier: 8.003A  pdb=" N   ASN C 279 " --> pdb=" O   GLN B 276 " (cutoff:3.500A)
      removed outlier: 6.180A  pdb=" N   ILE B 278 " --> pdb=" O   ASN C 279 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   GLN A 276 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
      removed outlier: 8.005A  pdb=" N   ASN B 279 " --> pdb=" O   GLN A 276 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   ILE A 278 " --> pdb=" O   ASN B 279 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   VAL A 275 " --> pdb=" O   GLN D 276 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   ILE D 278 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   ILE A 277 " --> pdb=" O   ILE D 278 " (cutoff:3.500A)
      removed outlier: 8.202A  pdb=" N   LYS D 280 " --> pdb=" O   ILE A 277 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ASN A 279 " --> pdb=" O   LYS D 280 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 284 through 289
      removed outlier: 6.543A  pdb=" N   SER B 285 " --> pdb=" O   ASN C 286 " (cutoff:3.500A)
      removed outlier: 7.967A  pdb=" N   GLN C 288 " --> pdb=" O   SER B 285 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   VAL B 287 " --> pdb=" O   GLN C 288 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   SER A 285 " --> pdb=" O   ASN B 286 " (cutoff:3.500A)
      removed outlier: 7.957A  pdb=" N   GLN B 288 " --> pdb=" O   SER A 285 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   VAL A 287 " --> pdb=" O   GLN B 288 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 294 through 299
      removed outlier: 8.975A  pdb=" N   LYS B 294 " --> pdb=" O   ASP C 295 " (cutoff:3.500A)
      removed outlier: 8.956A  pdb=" N   ILE C 297 " --> pdb=" O   LYS B 294 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   ASN B 296 " --> pdb=" O   ILE C 297 " (cutoff:3.500A)
      removed outlier: 7.896A  pdb=" N   HIS C 299 " --> pdb=" O   ASN B 296 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   LYS B 298 " --> pdb=" O   HIS C 299 " (cutoff:3.500A)
      removed outlier: 8.965A  pdb=" N   LYS A 294 " --> pdb=" O   ASP B 295 " (cutoff:3.500A)
      removed outlier: 8.946A  pdb=" N   ILE B 297 " --> pdb=" O   LYS A 294 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   ASN A 296 " --> pdb=" O   ILE B 297 " (cutoff:3.500A)
      removed outlier: 7.888A  pdb=" N   HIS B 299 " --> pdb=" O   ASN A 296 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   LYS A 298 " --> pdb=" O   HIS B 299 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   ASP A 295 " --> pdb=" O   LYS D 294 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   ASN D 296 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   ASP D 295 " --> pdb=" O   LYS E 294 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   ASN E 296 " --> pdb=" O   ASP D 295 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 307 through 310
      removed outlier: 6.562A  pdb=" N   GLN B 307 " --> pdb=" O   ILE C 308 " (cutoff:3.500A)
      removed outlier: 7.541A  pdb=" N   TYR C 310 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   VAL B 309 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   GLN A 307 " --> pdb=" O   ILE B 308 " (cutoff:3.500A)
      removed outlier: 7.547A  pdb=" N   TYR B 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   VAL A 309 " --> pdb=" O   TYR B 310 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 313 through 314
      removed outlier: 6.842A  pdb=" N   VAL B 313 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
      removed outlier: 6.847A  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 320
      removed outlier: 6.557A  pdb=" N   LYS B 317 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
      removed outlier: 7.520A  pdb=" N   SER C 320 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   THR B 319 " --> pdb=" O   SER C 320 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   LYS A 317 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 7.528A  pdb=" N   SER B 320 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   THR A 319 " --> pdb=" O   SER B 320 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 336 through 337
      removed outlier: 6.208A  pdb=" N   GLN A 336 " --> pdb=" O   VAL D 337 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   GLN D 336 " --> pdb=" O   VAL E 337 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 340 through 345
      removed outlier: 6.419A  pdb=" N   LYS B 340 " --> pdb=" O   SER C 341 " (cutoff:3.500A)
      removed outlier: 8.097A  pdb=" N   LYS C 343 " --> pdb=" O   LYS B 340 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   GLU B 342 " --> pdb=" O   LYS C 343 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   ASP C 345 " --> pdb=" O   GLU B 342 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   LEU B 344 " --> pdb=" O   ASP C 345 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   LYS A 340 " --> pdb=" O   SER B 341 " (cutoff:3.500A)
      removed outlier: 8.078A  pdb=" N   LYS B 343 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   GLU A 342 " --> pdb=" O   LYS B 343 " (cutoff:3.500A)
      removed outlier: 7.886A  pdb=" N   ASP B 345 " --> pdb=" O   GLU A 342 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   LEU A 344 " --> pdb=" O   ASP B 345 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 348 through 354
      removed outlier: 6.345A  pdb=" N   ARG A 349 " --> pdb=" O   VAL D 350 " (cutoff:3.500A)
      removed outlier: 7.937A  pdb=" N   SER D 352 " --> pdb=" O   ARG A 349 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   GLN A 351 " --> pdb=" O   SER D 352 " (cutoff:3.500A)
      removed outlier: 8.252A  pdb=" N   ILE D 354 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   LYS A 353 " --> pdb=" O   ILE D 354 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   ARG D 349 " --> pdb=" O   VAL E 350 " (cutoff:3.500A)
      removed outlier: 7.929A  pdb=" N   SER E 352 " --> pdb=" O   ARG D 349 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   GLN D 351 " --> pdb=" O   SER E 352 " (cutoff:3.500A)
      removed outlier: 8.245A  pdb=" N   ILE E 354 " --> pdb=" O   GLN D 351 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   LYS D 353 " --> pdb=" O   ILE E 354 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 357 through 362
      removed outlier: 6.572A  pdb=" N   ASP A 358 " --> pdb=" O   ASN D 359 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   THR D 361 " --> pdb=" O   ASP A 358 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   ILE A 360 " --> pdb=" O   THR D 361 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   ASP D 358 " --> pdb=" O   ASN E 359 " (cutoff:3.500A)
      removed outlier: 7.715A  pdb=" N   THR E 361 " --> pdb=" O   ASP D 358 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   ILE D 360 " --> pdb=" O   THR E 361 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 368 through 373
      removed outlier: 6.220A  pdb=" N   ASN A 368 " --> pdb=" O   LYS D 369 " (cutoff:3.500A)
      removed outlier: 7.691A  pdb=" N   ILE D 371 " --> pdb=" O   ASN A 368 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   LYS A 370 " --> pdb=" O   ILE D 371 " (cutoff:3.500A)
      removed outlier: 7.834A  pdb=" N   THR D 373 " --> pdb=" O   LYS A 370 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   GLU A 372 " --> pdb=" O   THR D 373 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   ASN D 368 " --> pdb=" O   LYS E 369 " (cutoff:3.500A)
      removed outlier: 7.697A  pdb=" N   ILE E 371 " --> pdb=" O   ASN D 368 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   LYS D 370 " --> pdb=" O   ILE E 371 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   THR E 373 " --> pdb=" O   LYS D 370 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   GLU D 372 " --> pdb=" O   THR E 373 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 376 through 379
      removed outlier: 6.642A  pdb=" N   LEU B 376 " --> pdb=" O   THR C 377 " (cutoff:3.500A)
      removed outlier: 8.098A  pdb=" N   ARG C 379 " --> pdb=" O   LEU B 376 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   PHE B 378 " --> pdb=" O   ARG C 379 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   LEU A 376 " --> pdb=" O   THR B 377 " (cutoff:3.500A)
      removed outlier: 8.098A  pdb=" N   ARG B 379 " --> pdb=" O   LEU A 376 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   PHE A 378 " --> pdb=" O   ARG B 379 " (cutoff:3.500A)

    85 hydrogen bonds defined for protein.
    255 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: 0.65

  Time building geometry restraints manager: 0.42 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: 1395
        1.34 -     1.46: 624
        1.46 -     1.57: 2171
        1.57 -     1.69: 0
        1.69 -     1.81: 10
  Bond restraints: 4200
  Sorted by residual:
  bond pdb=" N   LYS A 317 "
       pdb=" CA  LYS A 317 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.22e-02 6.72e+03 6.19e+00
  bond pdb=" N   ARG E 349 "
       pdb=" CA  ARG E 349 "
    ideal  model  delta    sigma   weight residual
    1.462  1.492 -0.029 1.20e-02 6.94e+03 6.04e+00
  bond pdb=" N   LYS B 317 "
       pdb=" CA  LYS B 317 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.030 1.22e-02 6.72e+03 5.93e+00
  bond pdb=" N   LYS C 317 "
       pdb=" CA  LYS C 317 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.030 1.22e-02 6.72e+03 5.91e+00
  bond pdb=" N   LYS E 317 "
       pdb=" CA  LYS E 317 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 1.22e-02 6.72e+03 5.81e+00
  ... (remaining 4195 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 5487
        1.73 -     3.47: 103
        3.47 -     5.20: 15
        5.20 -     6.93: 0
        6.93 -     8.67: 5
  Bond angle restraints: 5610
  Sorted by residual:
  angle pdb=" CA  LEU B 315 "
        pdb=" CB  LEU B 315 "
        pdb=" CG  LEU B 315 "
      ideal   model   delta    sigma   weight residual
     116.30  124.97   -8.67 3.50e+00 8.16e-02 6.13e+00
  angle pdb=" CA  LEU A 315 "
        pdb=" CB  LEU A 315 "
        pdb=" CG  LEU A 315 "
      ideal   model   delta    sigma   weight residual
     116.30  124.96   -8.66 3.50e+00 8.16e-02 6.12e+00
  angle pdb=" CA  LEU E 315 "
        pdb=" CB  LEU E 315 "
        pdb=" CG  LEU E 315 "
      ideal   model   delta    sigma   weight residual
     116.30  124.95   -8.65 3.50e+00 8.16e-02 6.11e+00
  angle pdb=" CA  LEU C 315 "
        pdb=" CB  LEU C 315 "
        pdb=" CG  LEU C 315 "
      ideal   model   delta    sigma   weight residual
     116.30  124.95   -8.65 3.50e+00 8.16e-02 6.11e+00
  angle pdb=" CA  LEU D 315 "
        pdb=" CB  LEU D 315 "
        pdb=" CG  LEU D 315 "
      ideal   model   delta    sigma   weight residual
     116.30  124.95   -8.65 3.50e+00 8.16e-02 6.11e+00
  ... (remaining 5605 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.96: 2229
       11.96 -    23.92: 216
       23.92 -    35.88: 100
       35.88 -    47.84: 21
       47.84 -    59.80: 14
  Dihedral angle restraints: 2580
    sinusoidal: 1080
      harmonic: 1500
  Sorted by residual:
  dihedral pdb=" CG  LYS D 331 "
           pdb=" CD  LYS D 331 "
           pdb=" CE  LYS D 331 "
           pdb=" NZ  LYS D 331 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.80  -59.80     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CG  LYS A 331 "
           pdb=" CD  LYS A 331 "
           pdb=" CE  LYS A 331 "
           pdb=" NZ  LYS A 331 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.77  -59.77     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CG  LYS C 331 "
           pdb=" CD  LYS C 331 "
           pdb=" CE  LYS C 331 "
           pdb=" NZ  LYS C 331 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.76  -59.76     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 2577 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 310
       0.025 -    0.050: 167
       0.050 -    0.075: 38
       0.075 -    0.101: 64
       0.101 -    0.126: 46
  Chirality restraints: 625
  Sorted by residual:
  chirality pdb=" CA  LYS C 340 "
            pdb=" N   LYS C 340 "
            pdb=" C   LYS C 340 "
            pdb=" CB  LYS C 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.64   -0.13 2.00e-01 2.50e+01 3.95e-01
  chirality pdb=" CA  LYS D 340 "
            pdb=" N   LYS D 340 "
            pdb=" C   LYS D 340 "
            pdb=" CB  LYS D 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.63   -0.12 2.00e-01 2.50e+01 3.83e-01
  chirality pdb=" CA  ILE E 277 "
            pdb=" N   ILE E 277 "
            pdb=" C   ILE E 277 "
            pdb=" CB  ILE E 277 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.74e-01
  ... (remaining 622 not shown)

  Planarity restraints: 725
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 300 "    0.016 5.00e-02 4.00e+02   2.46e-02 9.69e-01
        pdb=" N   PRO C 301 "   -0.043 5.00e-02 4.00e+02
        pdb=" CA  PRO C 301 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO C 301 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL E 300 "    0.016 5.00e-02 4.00e+02   2.45e-02 9.61e-01
        pdb=" N   PRO E 301 "   -0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO E 301 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO E 301 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 300 "    0.016 5.00e-02 4.00e+02   2.43e-02 9.48e-01
        pdb=" N   PRO A 301 "   -0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO A 301 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 301 "    0.013 5.00e-02 4.00e+02
  ... (remaining 722 not shown)

  Histogram of nonbonded interaction distances:
        2.38 -     2.88: 1459
        2.88 -     3.39: 3289
        3.39 -     3.89: 7295
        3.89 -     4.40: 7622
        4.40 -     4.90: 15606
  Nonbonded interactions: 35271
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 346 "
            pdb=" NZ  LYS B 311 "
     model   vdw
     2.381 3.120
  nonbonded pdb=" O   PHE B 346 "
            pdb=" NZ  LYS C 311 "
     model   vdw
     2.398 3.120
  nonbonded pdb=" NZ  LYS A 311 "
            pdb=" O   PHE D 346 "
     model   vdw
     2.398 3.120
  nonbonded pdb=" NZ  LYS D 311 "
            pdb=" O   PHE E 346 "
     model   vdw
     2.404 3.120
  nonbonded pdb=" ND1 HIS E 299 "
            pdb=" OH  TYR E 310 "
     model   vdw
     2.475 3.120
  ... (remaining 35266 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:             3.490
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.500
  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:9.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
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   0.055   4200  Z= 0.201
  Angle     :  0.627   8.666   5610  Z= 0.319
  Chirality :  0.050   0.126    625
  Planarity :  0.003   0.025    725
  Dihedral  : 12.602  59.802   1630
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 2.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.29), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.21 (0.22), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 349 
 TYR   0.004   0.001   TYR B 310 
 PHE   0.004   0.001   PHE A 378 
 HIS   0.003   0.001   HIS D 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 4200)
  covalent geometry    : angle       0.62703 ( 5610)
  hydrogen bonds       : bond        0.10235 (   85)
  hydrogen bonds       : angle       7.09345 (  255)

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.123 
Fit side-chains
REVERT: C  316 SER cc_start: 0.8478 (p) cc_final: 0.8222 (m)
REVERT: D  307 GLN cc_start: 0.8115 (mt0) cc_final: 0.7860 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.5253
  time to fit residues: 69.5316
Evaluate side-chains
  99 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    7.9990
   chunk 16 optimal weight:    9.9990
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0670
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.9922

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

Flipped N/Q/H residues before XYZ refinement:
A 296 ASN
A 381 ASN
B 276 GLN
B 296 ASN
B 359 ASN
B 381 ASN
C 276 GLN
C 296 ASN
C 359 ASN
C 381 ASN
D 296 ASN
D 359 ASN
D 368 ASN
D 381 ASN
E 359 ASN
E 381 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.093609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.079619 restraints weight = 5864.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 2.28
r_work: 0.3177 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.1437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4200  Z= 0.121
  Angle     :  0.569   9.186   5610  Z= 0.266
  Chirality :  0.050   0.158    625
  Planarity :  0.002   0.017    725
  Dihedral  :  4.043  13.308    560
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 12.21 %
    Favored  : 86.74 %
  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 (0.30), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.12 (0.23), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 349 
 TYR   0.009   0.001   TYR D 310 
 PHE   0.007   0.001   PHE D 378 
 HIS   0.005   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 4200)
  covalent geometry    : angle       0.56918 ( 5610)
  hydrogen bonds       : bond        0.01922 (   85)
  hydrogen bonds       : angle       4.82235 (  255)

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 111
  time to evaluate  : 0.159 
Fit side-chains
  outliers start: 5
  outliers final: 1
  residues processed: 111
  average time/residue: 0.4575
  time to fit residues: 52.7089
Evaluate side-chains
  97 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 96
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  316 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 10 optimal weight:    7.9990
   chunk 30 optimal weight:    3.9990
   chunk 6 optimal weight:    9.9990
   chunk 42 optimal weight:    7.9990
   chunk 7 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   chunk 46 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 51 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   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 276 GLN
A 368 ASN
A 381 ASN
B 276 GLN
B 296 ASN
B 381 ASN
C 296 ASN
C 359 ASN
C 368 ASN
C 381 ASN
D 381 ASN
E 307 GLN
E 359 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.089183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.075411 restraints weight = 6008.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 2.26
r_work: 0.3125 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3012 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.1776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   4200  Z= 0.279
  Angle     :  0.644   9.646   5610  Z= 0.303
  Chirality :  0.050   0.124    625
  Planarity :  0.002   0.023    725
  Dihedral  :  4.294  12.200    560
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 16.21 %
    Favored  : 82.32 %
  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 (0.29), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.22), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.001   ARG A 349 
 TYR   0.011   0.002   TYR E 310 
 PHE   0.012   0.002   PHE D 378 
 HIS   0.004   0.001   HIS C 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00645 ( 4200)
  covalent geometry    : angle       0.64436 ( 5610)
  hydrogen bonds       : bond        0.02325 (   85)
  hydrogen bonds       : angle       4.57627 (  255)

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.144 
Fit side-chains
  outliers start: 7
  outliers final: 4
  residues processed: 103
  average time/residue: 0.4354
  time to fit residues: 46.6799
Evaluate side-chains
  97 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 93
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  276 GLN
Chi-restraints excluded: chain C residue  297 ILE
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain E residue  357 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 50 optimal weight:    0.0980
   chunk 19 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    1.0188

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
A 381 ASN
B 276 GLN
B 296 ASN
B 359 ASN
B 381 ASN
C 359 ASN
C 381 ASN
D 359 ASN
D 381 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.092198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.078320 restraints weight = 5815.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 2.27
r_work: 0.3183 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4200  Z= 0.122
  Angle     :  0.571   8.993   5610  Z= 0.266
  Chirality :  0.050   0.157    625
  Planarity :  0.002   0.008    725
  Dihedral  :  4.112  12.142    560
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 18.11 %
    Favored  : 80.84 %
  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 (0.29), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.12 (0.22), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 349 
 TYR   0.007   0.001   TYR D 310 
 PHE   0.007   0.001   PHE D 378 
 HIS   0.004   0.001   HIS C 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 4200)
  covalent geometry    : angle       0.57055 ( 5610)
  hydrogen bonds       : bond        0.01556 (   85)
  hydrogen bonds       : angle       4.36496 (  255)

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 100
  time to evaluate  : 0.166 
Fit side-chains
  outliers start: 5
  outliers final: 3
  residues processed: 102
  average time/residue: 0.3913
  time to fit residues: 41.6500
Evaluate side-chains
  98 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 95
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  297 ILE
Chi-restraints excluded: chain C residue  379 ARG
Chi-restraints excluded: chain D residue  356 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 41 optimal weight:    7.9990
   chunk 42 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 18 optimal weight:    9.9990
   chunk 2 optimal weight:    7.9990
   chunk 14 optimal weight:    0.0170
   chunk 11 optimal weight:    9.9990
   chunk 27 optimal weight:    5.9990
   chunk 40 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    3.6026

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

Flipped N/Q/H residues before XYZ refinement:
** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 368 ASN
A 381 ASN
** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 296 ASN
B 307 GLN
B 359 ASN
B 381 ASN
C 359 ASN
C 381 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.088513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.074610 restraints weight = 5879.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 2.19
r_work: 0.3108 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2998 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.039   4200  Z= 0.326
  Angle     :  0.645   9.128   5610  Z= 0.310
  Chirality :  0.050   0.144    625
  Planarity :  0.002   0.023    725
  Dihedral  :  4.392  13.267    560
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 20.00 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.88 (0.29), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.19 (0.22), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 349 
 TYR   0.012   0.002   TYR E 310 
 PHE   0.012   0.002   PHE D 378 
 HIS   0.004   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00754 ( 4200)
  covalent geometry    : angle       0.64537 ( 5610)
  hydrogen bonds       : bond        0.02215 (   85)
  hydrogen bonds       : angle       4.36372 (  255)

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.185 
Fit side-chains
  outliers start: 9
  outliers final: 6
  residues processed: 102
  average time/residue: 0.4185
  time to fit residues: 44.6390
Evaluate side-chains
  104 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  297 ILE
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain C residue  379 ARG
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain E residue  357 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 381 ASN
B 276 GLN
B 296 ASN
B 381 ASN
C 359 ASN
C 381 ASN
D 359 ASN
D 381 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.093273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.079717 restraints weight = 5553.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.16
r_work: 0.3141 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3022 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
moved from start:          0.2076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4200  Z= 0.168
  Angle     :  0.597   8.891   5610  Z= 0.278
  Chirality :  0.050   0.159    625
  Planarity :  0.002   0.012    725
  Dihedral  :  4.257  12.433    560
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 20.63 %
    Favored  : 77.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.86 (0.29), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.17 (0.22), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 349 
 TYR   0.007   0.002   TYR D 310 
 PHE   0.008   0.001   PHE D 378 
 HIS   0.005   0.001   HIS C 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 4200)
  covalent geometry    : angle       0.59690 ( 5610)
  hydrogen bonds       : bond        0.01686 (   85)
  hydrogen bonds       : angle       4.21918 (  255)

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.174 
Fit side-chains
  outliers start: 7
  outliers final: 3
  residues processed: 103
  average time/residue: 0.4059
  time to fit residues: 43.6928
Evaluate side-chains
  97 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 94
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  297 ILE
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain C residue  379 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 37 optimal weight:    7.9990
   chunk 20 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 11 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   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 381 ASN
B 276 GLN
B 296 ASN
B 381 ASN
C 359 ASN
C 381 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.093766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.080057 restraints weight = 5587.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 2.16
r_work: 0.3158 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3040 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.2103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4200  Z= 0.149
  Angle     :  0.571   9.599   5610  Z= 0.270
  Chirality :  0.049   0.124    625
  Planarity :  0.002   0.012    725
  Dihedral  :  4.140  11.961    560
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 20.84 %
    Favored  : 77.68 %
  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 (0.29), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.22), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 349 
 TYR   0.007   0.002   TYR D 310 
 PHE   0.008   0.001   PHE D 378 
 HIS   0.004   0.001   HIS C 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 4200)
  covalent geometry    : angle       0.57123 ( 5610)
  hydrogen bonds       : bond        0.01543 (   85)
  hydrogen bonds       : angle       4.12261 (  255)

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 98
  time to evaluate  : 0.181 
Fit side-chains
REVERT: C  282 LEU cc_start: 0.9296 (mt) cc_final: 0.9073 (mp)
REVERT: E  289 SER cc_start: 0.9116 (t) cc_final: 0.8744 (p)
REVERT: E  325 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9124 (tt)
  outliers start: 7
  outliers final: 4
  residues processed: 102
  average time/residue: 0.3681
  time to fit residues: 39.4216
Evaluate side-chains
  99 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  297 ILE
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain C residue  379 ARG
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain E residue  325 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 42 optimal weight:    6.9990
   chunk 49 optimal weight:    7.9990
   chunk 17 optimal weight:    0.6980
   chunk 35 optimal weight:    7.9990
   chunk 12 optimal weight:   10.0000
   chunk 47 optimal weight:    6.9990
   chunk 53 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 27 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   overall best weight:    3.1388

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

Flipped N/Q/H residues before XYZ refinement:
** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 381 ASN
B 276 GLN
B 296 ASN
B 359 ASN
B 381 ASN
C 359 ASN
C 381 ASN
D 381 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.091131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.077535 restraints weight = 5589.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 2.13
r_work: 0.3117 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2997 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8560
moved from start:          0.2160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.052   4200  Z= 0.290
  Angle     :  0.633   8.861   5610  Z= 0.306
  Chirality :  0.050   0.154    625
  Planarity :  0.002   0.019    725
  Dihedral  :  4.359  16.357    560
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 20.21 %
    Favored  : 77.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.93 (0.29), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.22 (0.22), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG D 379 
 TYR   0.011   0.002   TYR E 310 
 PHE   0.010   0.002   PHE D 378 
 HIS   0.004   0.001   HIS C 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00671 ( 4200)
  covalent geometry    : angle       0.63306 ( 5610)
  hydrogen bonds       : bond        0.02000 (   85)
  hydrogen bonds       : angle       4.24811 (  255)

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.165 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8530 (tt)
REVERT: C  282 LEU cc_start: 0.9296 (mt) cc_final: 0.9087 (mp)
  outliers start: 9
  outliers final: 5
  residues processed: 99
  average time/residue: 0.3884
  time to fit residues: 40.2584
Evaluate side-chains
  98 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain C residue  297 ILE
Chi-restraints excluded: chain C residue  379 ARG
Chi-restraints excluded: chain D residue  300 VAL
Chi-restraints excluded: chain E residue  300 VAL
Chi-restraints excluded: chain E residue  357 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 38 optimal weight:    9.9990
   chunk 5 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 12 optimal weight:    9.9990
   chunk 34 optimal weight:    0.6980
   chunk 33 optimal weight:    6.9990
   chunk 47 optimal weight:    5.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 381 ASN
B 276 GLN
B 359 ASN
B 381 ASN
C 359 ASN
C 381 ASN
D 381 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.093479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.079871 restraints weight = 5647.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 2.17
r_work: 0.3158 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4200  Z= 0.144
  Angle     :  0.591   9.653   5610  Z= 0.279
  Chirality :  0.050   0.165    625
  Planarity :  0.002   0.011    725
  Dihedral  :  4.211  15.415    560
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 21.47 %
    Favored  : 76.84 %
  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: -2.85 (0.29), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.17 (0.22), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 379 
 TYR   0.006   0.001   TYR D 310 
 PHE   0.007   0.001   PHE D 378 
 HIS   0.004   0.001   HIS C 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 4200)
  covalent geometry    : angle       0.59062 ( 5610)
  hydrogen bonds       : bond        0.01496 (   85)
  hydrogen bonds       : angle       4.13034 (  255)

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.171 
Fit side-chains
REVERT: C  282 LEU cc_start: 0.9272 (mt) cc_final: 0.9059 (mp)
REVERT: E  289 SER cc_start: 0.9127 (t) cc_final: 0.8768 (p)
  outliers start: 8
  outliers final: 3
  residues processed: 100
  average time/residue: 0.4136
  time to fit residues: 43.2962
Evaluate side-chains
  94 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 91
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  297 ILE
Chi-restraints excluded: chain C residue  379 ARG
Chi-restraints excluded: chain D residue  300 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 41 optimal weight:    8.9990
   chunk 38 optimal weight:   10.0000
   chunk 31 optimal weight:    0.7980
   chunk 16 optimal weight:    8.9990
   chunk 52 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0970
   chunk 17 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
A 381 ASN
B 276 GLN
B 359 ASN
B 381 ASN
C 359 ASN
C 381 ASN
D 381 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.095724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.082182 restraints weight = 5431.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 2.14
r_work: 0.3204 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3086 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.2194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4200  Z= 0.104
  Angle     :  0.565   8.054   5610  Z= 0.269
  Chirality :  0.050   0.120    625
  Planarity :  0.002   0.013    725
  Dihedral  :  4.033  14.273    560
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 21.89 %
    Favored  : 77.05 %
  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 (0.29), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.12 (0.22), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 379 
 TYR   0.006   0.001   TYR D 310 
 PHE   0.006   0.001   PHE D 378 
 HIS   0.004   0.001   HIS C 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 4200)
  covalent geometry    : angle       0.56514 ( 5610)
  hydrogen bonds       : bond        0.01263 (   85)
  hydrogen bonds       : angle       4.06670 (  255)

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.162 
Fit side-chains
REVERT: C  282 LEU cc_start: 0.9238 (mt) cc_final: 0.9010 (mp)
REVERT: E  289 SER cc_start: 0.9095 (t) cc_final: 0.8752 (p)
  outliers start: 5
  outliers final: 2
  residues processed: 101
  average time/residue: 0.4331
  time to fit residues: 45.6044
Evaluate side-chains
  98 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 96
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  379 ARG
Chi-restraints excluded: chain D residue  300 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 46 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 38 optimal weight:    9.9990
   chunk 51 optimal weight:    7.9990
   chunk 28 optimal weight:    7.9990
   chunk 41 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0000
   chunk 13 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    1.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 381 ASN
B 276 GLN
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
B 381 ASN
C 359 ASN
C 381 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.095019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.081364 restraints weight = 5528.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 2.15
r_work: 0.3188 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4200  Z= 0.135
  Angle     :  0.582   9.590   5610  Z= 0.276
  Chirality :  0.049   0.119    625
  Planarity :  0.002   0.012    725
  Dihedral  :  4.052  14.027    560
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 22.32 %
    Favored  : 76.84 %
  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 (0.29), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.13 (0.22), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 379 
 TYR   0.007   0.002   TYR E 310 
 PHE   0.007   0.001   PHE D 378 
 HIS   0.004   0.001   HIS C 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 4200)
  covalent geometry    : angle       0.58240 ( 5610)
  hydrogen bonds       : bond        0.01432 (   85)
  hydrogen bonds       : angle       4.03905 (  255)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1596.26 seconds
wall clock time: 28 minutes 4.24 seconds (1684.24 seconds total)