Starting phenix.real_space_refine
on Thu Mar  6 00:23:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p65_13218/03_2025/7p65_13218.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p65_13218/03_2025/7p65_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_2025/7p65_13218.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p65_13218/03_2025/7p65_13218.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p65_13218/03_2025/7p65_13218.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p65_13218/03_2025/7p65_13218.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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:
    C, B, E, D
  Time building chain proxies: 2.91, per 1000 atoms: 0.70
  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: 0.99
  Conformation dependent library (CDL) restraints added in 551.3 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: 0.68
  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: 1.14

  Time building geometry restraints manager: 1.19 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.750
  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:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.870
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:15.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.520
-------------------------------------------------------------------------------
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= 0.263
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.90 (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
 HIS   0.003   0.001   HIS D 299 
 PHE   0.004   0.001   PHE A 378 
 TYR   0.004   0.001   TYR B 310 
 ARG   0.002   0.001   ARG B 349 

*********************** 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  : 0.486 
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: 1.1951
  time to fit residues: 158.6735
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  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 41 optimal weight:    6.9990
   chunk 23 optimal weight:    7.9990
   chunk 14 optimal weight:    0.4980
   chunk 28 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   chunk 26 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 49 optimal weight:    8.9990
   overall best weight:    3.2988

-------------------------------------------------------------------------------
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 = 0.3432 r_free = 0.3432 target = 0.089865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.076129 restraints weight = 5807.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 2.17
r_work: 0.3119 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.1602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.054   4200  Z= 0.469
  Angle     :  0.663  10.211   5610  Z= 0.314
  Chirality :  0.051   0.150    625
  Planarity :  0.003   0.016    725
  Dihedral  :  4.359  12.937    560
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 11.37 %
    Favored  : 86.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.79 (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
 HIS   0.005   0.001   HIS B 299 
 PHE   0.013   0.002   PHE D 378 
 TYR   0.010   0.002   TYR A 310 
 ARG   0.002   0.001   ARG B 349 

*********************** 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
  112 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.489 
Fit side-chains
REVERT: A  283 ASP cc_start: 0.8513 (t70) cc_final: 0.8272 (t0)
  outliers start: 8
  outliers final: 4
  residues processed: 105
  average time/residue: 0.8587
  time to fit residues: 94.3847
Evaluate side-chains
  101 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain B residue  276 GLN
Chi-restraints excluded: chain D residue  356 SER
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 54 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 17 optimal weight:    0.4980
   chunk 7 optimal weight:    4.9990
   chunk 39 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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
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: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.092196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.078417 restraints weight = 5814.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 2.25
r_work: 0.3181 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3069 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.1720

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= 0.188
  Angle     :  0.577   9.421   5610  Z= 0.267
  Chirality :  0.050   0.151    625
  Planarity :  0.002   0.008    725
  Dihedral  :  4.161  12.754    560
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  : 15.37 %
    Favored  : 84.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.78 (0.29), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.11 (0.22), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 299 
 PHE   0.007   0.001   PHE D 378 
 TYR   0.007   0.001   TYR D 310 
 ARG   0.001   0.000   ARG C 379 

*********************** 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
  103 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 101
  time to evaluate  : 0.521 
Fit side-chains
REVERT: A  283 ASP cc_start: 0.8503 (t70) cc_final: 0.8235 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 102
  average time/residue: 0.8936
  time to fit residues: 95.3951
Evaluate side-chains
  93 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 13 optimal weight:    7.9990
   chunk 44 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 18 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9980
   chunk 38 optimal weight:    8.9990
   chunk 36 optimal weight:    4.9990
   chunk 50 optimal weight:    0.2980
   chunk 16 optimal weight:   10.0000
   overall best weight:    1.4586

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 296 ASN
B 359 ASN
B 381 ASN
C 296 ASN
C 359 ASN
C 381 ASN
** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.091433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.077617 restraints weight = 5892.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.26
r_work: 0.3167 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3055 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.1878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4200  Z= 0.239
  Angle     :  0.562   9.190   5610  Z= 0.264
  Chirality :  0.049   0.136    625
  Planarity :  0.002   0.010    725
  Dihedral  :  4.119  11.986    560
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 17.68 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.79 (0.30), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.11 (0.23), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C 299 
 PHE   0.008   0.001   PHE D 378 
 TYR   0.008   0.002   TYR D 310 
 ARG   0.001   0.000   ARG C 379 

*********************** 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
  107 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.481 
Fit side-chains
  outliers start: 8
  outliers final: 3
  residues processed: 101
  average time/residue: 1.0162
  time to fit residues: 107.0649
Evaluate side-chains
  99 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 96
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 SER
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 51 optimal weight:    7.9990
   chunk 30 optimal weight:    0.0050
   chunk 54 optimal weight:    5.9990
   chunk 34 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 50 optimal weight:    0.0770
   chunk 12 optimal weight:   10.0000
   chunk 40 optimal weight:    1.9990
   chunk 21 optimal weight:    7.9990
   chunk 47 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    1.4156

-------------------------------------------------------------------------------
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 296 ASN
B 359 ASN
B 381 ASN
C 359 ASN
C 381 ASN
D 381 ASN
E 288 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.095213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.081324 restraints weight = 5353.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 2.08
r_work: 0.3176 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3063 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.1914

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= 0.228
  Angle     :  0.548   8.881   5610  Z= 0.259
  Chirality :  0.049   0.137    625
  Planarity :  0.002   0.011    725
  Dihedral  :  4.064  11.634    560
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 18.53 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.78 (0.30), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.11 (0.23), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C 299 
 PHE   0.008   0.001   PHE D 378 
 TYR   0.008   0.002   TYR D 310 
 ARG   0.001   0.000   ARG C 379 

*********************** 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
  105 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 0.511 
Fit side-chains
REVERT: A  283 ASP cc_start: 0.8493 (t70) cc_final: 0.8281 (t0)
REVERT: E  289 SER cc_start: 0.9136 (t) cc_final: 0.8801 (p)
  outliers start: 6
  outliers final: 3
  residues processed: 100
  average time/residue: 1.0168
  time to fit residues: 106.1276
Evaluate side-chains
  96 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain C residue  379 ARG
Chi-restraints excluded: chain D residue  356 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 10 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 52 optimal weight:    7.9990
   chunk 40 optimal weight:    7.9990
   chunk 32 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 22 optimal weight:    6.9990
   overall best weight:    3.3588

-------------------------------------------------------------------------------
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 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 = 0.3444 r_free = 0.3444 target = 0.090931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.077466 restraints weight = 5593.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 2.13
r_work: 0.3104 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2984 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.2077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.044   4200  Z= 0.483
  Angle     :  0.642  10.024   5610  Z= 0.306
  Chirality :  0.050   0.128    625
  Planarity :  0.002   0.022    725
  Dihedral  :  4.350  13.454    560
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 18.74 %
    Favored  : 79.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.89 (0.29), 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
 HIS   0.004   0.001   HIS B 299 
 PHE   0.011   0.002   PHE D 378 
 TYR   0.011   0.002   TYR E 310 
 ARG   0.002   0.001   ARG A 349 

*********************** 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
  108 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.548 
Fit side-chains
  outliers start: 10
  outliers final: 2
  residues processed: 102
  average time/residue: 0.8641
  time to fit residues: 92.3116
Evaluate side-chains
  99 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 97
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain E residue  357 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 16 optimal weight:   10.0000
   chunk 29 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 276 GLN
A 368 ASN
A 381 ASN
B 296 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 = 0.3459 r_free = 0.3459 target = 0.092017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.078411 restraints weight = 5589.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 2.15
r_work: 0.3125 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   4200  Z= 0.332
  Angle     :  0.604   9.101   5610  Z= 0.287
  Chirality :  0.050   0.157    625
  Planarity :  0.002   0.016    725
  Dihedral  :  4.294  12.784    560
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 20.21 %
    Favored  : 78.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.91 (0.29), 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
 HIS   0.005   0.001   HIS C 299 
 PHE   0.009   0.001   PHE D 378 
 TYR   0.008   0.002   TYR E 310 
 ARG   0.001   0.000   ARG D 379 

*********************** 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
  103 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.466 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8499 (tt)
REVERT: C  282 LEU cc_start: 0.9311 (mt) cc_final: 0.9100 (mp)
  outliers start: 7
  outliers final: 3
  residues processed: 100
  average time/residue: 0.9857
  time to fit residues: 103.1008
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  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain C residue  297 ILE
Chi-restraints excluded: chain D residue  356 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   chunk 29 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 49 optimal weight:    8.9990
   chunk 45 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 21 optimal weight:    6.9990
   chunk 6 optimal weight:    8.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    2.9788

-------------------------------------------------------------------------------
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 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 = 0.3451 r_free = 0.3451 target = 0.091182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.077703 restraints weight = 5550.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.13
r_work: 0.3112 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.2150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   4200  Z= 0.432
  Angle     :  0.633  10.052   5610  Z= 0.304
  Chirality :  0.050   0.120    625
  Planarity :  0.002   0.023    725
  Dihedral  :  4.403  13.628    560
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 19.37 %
    Favored  : 78.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.98 (0.28), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.26 (0.22), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C 299 
 PHE   0.010   0.002   PHE D 378 
 TYR   0.010   0.002   TYR E 310 
 ARG   0.001   0.000   ARG A 349 

*********************** 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
  104 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.477 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8546 (tt)
REVERT: C  282 LEU cc_start: 0.9319 (mt) cc_final: 0.9115 (mp)
  outliers start: 9
  outliers final: 6
  residues processed: 100
  average time/residue: 0.8045
  time to fit residues: 84.4806
Evaluate side-chains
  100 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  356 SER
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 D residue  356 SER
Chi-restraints excluded: chain E residue  300 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 6 optimal weight:    8.9990
   chunk 21 optimal weight:    5.9990
   chunk 12 optimal weight:    8.9990
   chunk 40 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 50 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 52 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   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 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 368 ASN
A 381 ASN
B 381 ASN
C 359 ASN
C 381 ASN
D 381 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.090576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.076992 restraints weight = 5607.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 2.14
r_work: 0.3101 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2982 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.2185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.040   4200  Z= 0.487
  Angle     :  0.663   9.778   5610  Z= 0.319
  Chirality :  0.051   0.164    625
  Planarity :  0.002   0.025    725
  Dihedral  :  4.469  14.291    560
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.01 (0.28), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.29 (0.21), residues: 540

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

*********************** 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
  99 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.508 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8599 (tt)
  outliers start: 7
  outliers final: 6
  residues processed: 96
  average time/residue: 0.8510
  time to fit residues: 85.5984
Evaluate side-chains
  97 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  356 SER
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 27 optimal weight:    0.0170
   chunk 34 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 6 optimal weight:    0.1980
   chunk 54 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.8022

-------------------------------------------------------------------------------
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 296 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 = 0.3490 r_free = 0.3490 target = 0.093973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.080458 restraints weight = 5472.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 2.14
r_work: 0.3167 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3049 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.2199

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= 0.178
  Angle     :  0.602   9.825   5610  Z= 0.284
  Chirality :  0.050   0.134    625
  Planarity :  0.002   0.012    725
  Dihedral  :  4.227  12.304    560
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 21.68 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.91 (0.29), 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
 HIS   0.005   0.001   HIS C 299 
 PHE   0.007   0.001   PHE D 378 
 TYR   0.005   0.001   TYR E 310 
 ARG   0.001   0.000   ARG D 349 

********************** 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
  106 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.515 
Fit side-chains
REVERT: D  339 VAL cc_start: 0.8970 (t) cc_final: 0.8649 (m)
REVERT: E  289 SER cc_start: 0.9145 (t) cc_final: 0.8780 (p)
  outliers start: 6
  outliers final: 1
  residues processed: 104
  average time/residue: 0.8688
  time to fit residues: 94.7562
Evaluate side-chains
  98 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 36 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 49 optimal weight:    8.9990
   chunk 8 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 53 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 27 optimal weight:    5.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 381 ASN
C 296 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 = 0.3499 r_free = 0.3499 target = 0.094491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.080964 restraints weight = 5504.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 2.14
r_work: 0.3174 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.2200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4200  Z= 0.206
  Angle     :  0.596   8.435   5610  Z= 0.282
  Chirality :  0.050   0.137    625
  Planarity :  0.002   0.013    725
  Dihedral  :  4.143  12.164    560
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  : 22.32 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.91 (0.29), 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
 HIS   0.004   0.001   HIS C 299 
 PHE   0.007   0.001   PHE D 378 
 TYR   0.006   0.001   TYR D 310 
 ARG   0.001   0.000   ARG D 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3690.40 seconds
wall clock time: 65 minutes 56.74 seconds (3956.74 seconds total)