Starting phenix.real_space_refine
on Sat Aug 23 05:25:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q7y_18244/08_2025/8q7y_18244.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q7y_18244/08_2025/8q7y_18244.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q7y_18244/08_2025/8q7y_18244.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q7y_18244/08_2025/8q7y_18244.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q7y_18244/08_2025/8q7y_18244.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q7y_18244/08_2025/8q7y_18244.map"
  }
  resolution = 2.6
  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=   0.001 sd=   0.040
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      60      5.16       5
     C    6412      2.51       5
     N    1824      2.21       5
     O    1736      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10032
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2508
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 303, 2508
          Classifications: {'peptide': 303}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 284}
          Chain breaks: 11
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 1.36, per 1000 atoms: 0.14
  Number of scatterers: 10032
  At special positions: 0
  Unit cell: (126.99, 87.15, 80.51, 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      60     16.00
     O    1736      8.00
     N    1824      7.00
     C    6412      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: 0.92
  Conformation dependent library (CDL) restraints added in 345.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2256

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 20 sheets defined
      34.7% alpha, 14.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 90 through 94
    Processing helix  chain 'A' and resid 192 through 196
      removed outlier: 3.549A  pdb=" N   TYR A 196 " --> pdb=" O   ASP A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 341
    Processing helix  chain 'A' and resid 368 through 382
      removed outlier: 3.603A  pdb=" N   MET A 372 " --> pdb=" O   ASP A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 406
      removed outlier: 3.909A  pdb=" N   TYR A 399 " --> pdb=" O   HIS A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 426
      removed outlier: 3.942A  pdb=" N   LEU A 426 " --> pdb=" O   MET A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 431
      No H-bonds generated for 'chain 'A' and resid 429 through 431'
    Processing helix  chain 'A' and resid 432 through 448
      removed outlier: 3.701A  pdb=" N   ARG A 442 " --> pdb=" O   GLU A 438 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   MET A 443 " --> pdb=" O   ARG A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 479
      removed outlier: 3.575A  pdb=" N   LEU A 471 " --> pdb=" O   ASN A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 525
    Processing helix  chain 'A' and resid 548 through 559
    Processing helix  chain 'A' and resid 618 through 624
    Processing helix  chain 'B' and resid 90 through 94
    Processing helix  chain 'B' and resid 192 through 196
      removed outlier: 3.550A  pdb=" N   TYR B 196 " --> pdb=" O   ASP B 193 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 341
    Processing helix  chain 'B' and resid 368 through 382
      removed outlier: 3.602A  pdb=" N   MET B 372 " --> pdb=" O   ASP B 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 406
      removed outlier: 3.909A  pdb=" N   TYR B 399 " --> pdb=" O   HIS B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 426
      removed outlier: 3.942A  pdb=" N   LEU B 426 " --> pdb=" O   MET B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 431
      No H-bonds generated for 'chain 'B' and resid 429 through 431'
    Processing helix  chain 'B' and resid 432 through 448
      removed outlier: 3.701A  pdb=" N   ARG B 442 " --> pdb=" O   GLU B 438 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   MET B 443 " --> pdb=" O   ARG B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 479
      removed outlier: 3.575A  pdb=" N   LEU B 471 " --> pdb=" O   ASN B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 520 through 525
    Processing helix  chain 'B' and resid 548 through 559
    Processing helix  chain 'B' and resid 618 through 624
    Processing helix  chain 'C' and resid 90 through 94
    Processing helix  chain 'C' and resid 192 through 196
      removed outlier: 3.550A  pdb=" N   TYR C 196 " --> pdb=" O   ASP C 193 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 337 through 341
    Processing helix  chain 'C' and resid 368 through 382
      removed outlier: 3.603A  pdb=" N   MET C 372 " --> pdb=" O   ASP C 368 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 395 through 406
      removed outlier: 3.908A  pdb=" N   TYR C 399 " --> pdb=" O   HIS C 395 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 422 through 426
      removed outlier: 3.943A  pdb=" N   LEU C 426 " --> pdb=" O   MET C 423 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 429 through 431
      No H-bonds generated for 'chain 'C' and resid 429 through 431'
    Processing helix  chain 'C' and resid 432 through 448
      removed outlier: 3.701A  pdb=" N   ARG C 442 " --> pdb=" O   GLU C 438 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   MET C 443 " --> pdb=" O   ARG C 439 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 467 through 479
      removed outlier: 3.576A  pdb=" N   LEU C 471 " --> pdb=" O   ASN C 467 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 520 through 525
    Processing helix  chain 'C' and resid 548 through 559
    Processing helix  chain 'C' and resid 618 through 624
    Processing helix  chain 'D' and resid 90 through 94
    Processing helix  chain 'D' and resid 192 through 196
      removed outlier: 3.549A  pdb=" N   TYR D 196 " --> pdb=" O   ASP D 193 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 337 through 341
    Processing helix  chain 'D' and resid 368 through 382
      removed outlier: 3.602A  pdb=" N   MET D 372 " --> pdb=" O   ASP D 368 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 395 through 406
      removed outlier: 3.908A  pdb=" N   TYR D 399 " --> pdb=" O   HIS D 395 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 422 through 426
      removed outlier: 3.943A  pdb=" N   LEU D 426 " --> pdb=" O   MET D 423 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 429 through 431
      No H-bonds generated for 'chain 'D' and resid 429 through 431'
    Processing helix  chain 'D' and resid 432 through 448
      removed outlier: 3.702A  pdb=" N   ARG D 442 " --> pdb=" O   GLU D 438 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   MET D 443 " --> pdb=" O   ARG D 439 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 467 through 479
      removed outlier: 3.575A  pdb=" N   LEU D 471 " --> pdb=" O   ASN D 467 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 520 through 525
    Processing helix  chain 'D' and resid 548 through 559
    Processing helix  chain 'D' and resid 618 through 624
    Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24
    Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 89
      removed outlier: 3.796A  pdb=" N   ILE A 208 " --> pdb=" O   SER A  88 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 199
    Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 336
    Processing sheet with id=AA5, first strand: chain 'A' and resid 351 through 356
      removed outlier: 3.647A  pdb=" N   ALA A 386 " --> pdb=" O   ARG A 352 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   GLU A 412 " --> pdb=" O   CYS A 389 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   VAL A 409 " --> pdb=" O   ILE A 455 " (cutoff:3.500A)
      removed outlier: 7.865A  pdb=" N   SER A 457 " --> pdb=" O   VAL A 409 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   ASP A 411 " --> pdb=" O   SER A 457 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   GLN A 485 " --> pdb=" O   ILE A 454 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   TRP A 456 " --> pdb=" O   GLN A 485 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ILE A 498 " --> pdb=" O   VAL A 484 " (cutoff:3.500A)
      removed outlier: 6.036A  pdb=" N   ILE A 499 " --> pdb=" O   ILE A 534 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   CYS A 536 " --> pdb=" O   ILE A 499 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   LEU A 533 " --> pdb=" O   GLY A 564 " (cutoff:3.500A)
      removed outlier: 8.835A  pdb=" N   PHE A 566 " --> pdb=" O   LEU A 533 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   LEU A 535 " --> pdb=" O   PHE A 566 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 23 through 24
    Processing sheet with id=AA7, first strand: chain 'B' and resid 88 through 89
      removed outlier: 3.794A  pdb=" N   ILE B 208 " --> pdb=" O   SER B  88 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 198 through 199
    Processing sheet with id=AA9, first strand: chain 'B' and resid 335 through 336
    Processing sheet with id=AB1, first strand: chain 'B' and resid 351 through 356
      removed outlier: 3.647A  pdb=" N   ALA B 386 " --> pdb=" O   ARG B 352 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   GLU B 412 " --> pdb=" O   CYS B 389 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   VAL B 409 " --> pdb=" O   ILE B 455 " (cutoff:3.500A)
      removed outlier: 7.865A  pdb=" N   SER B 457 " --> pdb=" O   VAL B 409 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   ASP B 411 " --> pdb=" O   SER B 457 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   GLN B 485 " --> pdb=" O   ILE B 454 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   TRP B 456 " --> pdb=" O   GLN B 485 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE B 498 " --> pdb=" O   VAL B 484 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   ILE B 499 " --> pdb=" O   ILE B 534 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   CYS B 536 " --> pdb=" O   ILE B 499 " (cutoff:3.500A)
      removed outlier: 7.066A  pdb=" N   LEU B 533 " --> pdb=" O   GLY B 564 " (cutoff:3.500A)
      removed outlier: 8.835A  pdb=" N   PHE B 566 " --> pdb=" O   LEU B 533 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   LEU B 535 " --> pdb=" O   PHE B 566 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 23 through 24
    Processing sheet with id=AB3, first strand: chain 'C' and resid 88 through 89
      removed outlier: 3.795A  pdb=" N   ILE C 208 " --> pdb=" O   SER C  88 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 198 through 199
    Processing sheet with id=AB5, first strand: chain 'C' and resid 335 through 336
    Processing sheet with id=AB6, first strand: chain 'C' and resid 351 through 356
      removed outlier: 3.645A  pdb=" N   ALA C 386 " --> pdb=" O   ARG C 352 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   GLU C 412 " --> pdb=" O   CYS C 389 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   VAL C 409 " --> pdb=" O   ILE C 455 " (cutoff:3.500A)
      removed outlier: 7.865A  pdb=" N   SER C 457 " --> pdb=" O   VAL C 409 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   ASP C 411 " --> pdb=" O   SER C 457 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   GLN C 485 " --> pdb=" O   ILE C 454 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   TRP C 456 " --> pdb=" O   GLN C 485 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ILE C 498 " --> pdb=" O   VAL C 484 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   ILE C 499 " --> pdb=" O   ILE C 534 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   CYS C 536 " --> pdb=" O   ILE C 499 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   LEU C 533 " --> pdb=" O   GLY C 564 " (cutoff:3.500A)
      removed outlier: 8.836A  pdb=" N   PHE C 566 " --> pdb=" O   LEU C 533 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   LEU C 535 " --> pdb=" O   PHE C 566 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 23 through 24
    Processing sheet with id=AB8, first strand: chain 'D' and resid 88 through 89
      removed outlier: 3.795A  pdb=" N   ILE D 208 " --> pdb=" O   SER D  88 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 198 through 199
    Processing sheet with id=AC1, first strand: chain 'D' and resid 335 through 336
    Processing sheet with id=AC2, first strand: chain 'D' and resid 351 through 356
      removed outlier: 3.646A  pdb=" N   ALA D 386 " --> pdb=" O   ARG D 352 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   GLU D 412 " --> pdb=" O   CYS D 389 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   VAL D 409 " --> pdb=" O   ILE D 455 " (cutoff:3.500A)
      removed outlier: 7.866A  pdb=" N   SER D 457 " --> pdb=" O   VAL D 409 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   ASP D 411 " --> pdb=" O   SER D 457 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   GLN D 485 " --> pdb=" O   ILE D 454 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   TRP D 456 " --> pdb=" O   GLN D 485 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE D 498 " --> pdb=" O   VAL D 484 " (cutoff:3.500A)
      removed outlier: 6.036A  pdb=" N   ILE D 499 " --> pdb=" O   ILE D 534 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   CYS D 536 " --> pdb=" O   ILE D 499 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   LEU D 533 " --> pdb=" O   GLY D 564 " (cutoff:3.500A)
      removed outlier: 8.836A  pdb=" N   PHE D 566 " --> pdb=" O   LEU D 533 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   LEU D 535 " --> pdb=" O   PHE D 566 " (cutoff:3.500A)

    296 hydrogen bonds defined for protein.
    780 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: 1.07

  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: 3279
        1.34 -     1.46: 2431
        1.46 -     1.58: 4502
        1.58 -     1.69: 0
        1.69 -     1.81: 104
  Bond restraints: 10316
  Sorted by residual:
  bond pdb=" CB  ARG C 473 "
       pdb=" CG  ARG C 473 "
    ideal  model  delta    sigma   weight residual
    1.520  1.454  0.066 3.00e-02 1.11e+03 4.88e+00
  bond pdb=" CB  ARG B 473 "
       pdb=" CG  ARG B 473 "
    ideal  model  delta    sigma   weight residual
    1.520  1.454  0.066 3.00e-02 1.11e+03 4.84e+00
  bond pdb=" CB  ARG A 473 "
       pdb=" CG  ARG A 473 "
    ideal  model  delta    sigma   weight residual
    1.520  1.454  0.066 3.00e-02 1.11e+03 4.78e+00
  bond pdb=" CB  ARG D 473 "
       pdb=" CG  ARG D 473 "
    ideal  model  delta    sigma   weight residual
    1.520  1.455  0.065 3.00e-02 1.11e+03 4.71e+00
  bond pdb=" CD  ARG D 473 "
       pdb=" NE  ARG D 473 "
    ideal  model  delta    sigma   weight residual
    1.458  1.443  0.015 1.40e-02 5.10e+03 1.09e+00
  ... (remaining 10311 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 13717
        2.19 -     4.38: 193
        4.38 -     6.58: 30
        6.58 -     8.77: 16
        8.77 -    10.96: 4
  Bond angle restraints: 13960
  Sorted by residual:
  angle pdb=" C   TYR A 472 "
        pdb=" N   ARG A 473 "
        pdb=" CA  ARG A 473 "
      ideal   model   delta    sigma   weight residual
     122.38  113.87    8.51 1.81e+00 3.05e-01 2.21e+01
  angle pdb=" C   TYR C 472 "
        pdb=" N   ARG C 473 "
        pdb=" CA  ARG C 473 "
      ideal   model   delta    sigma   weight residual
     122.38  113.93    8.45 1.81e+00 3.05e-01 2.18e+01
  angle pdb=" C   TYR B 472 "
        pdb=" N   ARG B 473 "
        pdb=" CA  ARG B 473 "
      ideal   model   delta    sigma   weight residual
     122.38  113.96    8.42 1.81e+00 3.05e-01 2.17e+01
  angle pdb=" C   TYR D 472 "
        pdb=" N   ARG D 473 "
        pdb=" CA  ARG D 473 "
      ideal   model   delta    sigma   weight residual
     122.38  113.96    8.42 1.81e+00 3.05e-01 2.16e+01
  angle pdb=" N   PRO C 480 "
        pdb=" CD  PRO C 480 "
        pdb=" CG  PRO C 480 "
      ideal   model   delta    sigma   weight residual
     103.20   96.74    6.46 1.50e+00 4.44e-01 1.85e+01
  ... (remaining 13955 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.72: 4943
       17.72 -    35.43: 689
       35.43 -    53.15: 246
       53.15 -    70.87: 74
       70.87 -    88.58: 16
  Dihedral angle restraints: 5968
    sinusoidal: 2492
      harmonic: 3476
  Sorted by residual:
  dihedral pdb=" CA  ARG C 473 "
           pdb=" C   ARG C 473 "
           pdb=" N   TRP C 474 "
           pdb=" CA  TRP C 474 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.22   19.78     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  ARG D 473 "
           pdb=" C   ARG D 473 "
           pdb=" N   TRP D 474 "
           pdb=" CA  TRP D 474 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.24   19.76     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  ARG A 473 "
           pdb=" C   ARG A 473 "
           pdb=" N   TRP A 474 "
           pdb=" CA  TRP A 474 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.25   19.75     0      5.00e+00 4.00e-02 1.56e+01
  ... (remaining 5965 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 781
       0.026 -    0.051: 327
       0.051 -    0.077: 142
       0.077 -    0.103: 106
       0.103 -    0.128: 56
  Chirality restraints: 1412
  Sorted by residual:
  chirality pdb=" CA  ILE C 415 "
            pdb=" N   ILE C 415 "
            pdb=" C   ILE C 415 "
            pdb=" CB  ILE C 415 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.13e-01
  chirality pdb=" CA  ILE B 415 "
            pdb=" N   ILE B 415 "
            pdb=" C   ILE B 415 "
            pdb=" CB  ILE B 415 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.06e-01
  chirality pdb=" CA  ILE A 415 "
            pdb=" N   ILE A 415 "
            pdb=" C   ILE A 415 "
            pdb=" CB  ILE A 415 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.98e-01
  ... (remaining 1409 not shown)

  Planarity restraints: 1780
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C  63 "    0.022 5.00e-02 4.00e+02   3.31e-02 1.76e+00
        pdb=" N   PRO C  64 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO C  64 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C  64 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D  63 "   -0.022 5.00e-02 4.00e+02   3.29e-02 1.73e+00
        pdb=" N   PRO D  64 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO D  64 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO D  64 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A  63 "   -0.022 5.00e-02 4.00e+02   3.29e-02 1.73e+00
        pdb=" N   PRO A  64 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A  64 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A  64 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1777 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 164
        2.64 -     3.21: 8427
        3.21 -     3.77: 16021
        3.77 -     4.34: 23289
        4.34 -     4.90: 36076
  Nonbonded interactions: 83977
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG C 473 "
            pdb=" O   ASP D 469 "
     model   vdw
     2.081 3.120
  nonbonded pdb=" O   ASP C 469 "
            pdb=" NH2 ARG D 473 "
     model   vdw
     2.085 3.120
  nonbonded pdb=" NH2 ARG A 473 "
            pdb=" O   ASP B 469 "
     model   vdw
     2.096 3.120
  nonbonded pdb=" O   ASP A 469 "
            pdb=" NH2 ARG B 473 "
     model   vdw
     2.099 3.120
  nonbonded pdb=" OD2 ASP D 368 "
            pdb=" OG1 THR D 371 "
     model   vdw
     2.137 3.040
  ... (remaining 83972 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 'B'
  selection = chain 'C'
  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:             5.190
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.710
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.010
  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:6.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
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      :  0.003   0.066  10316  Z= 0.133
  Angle     :  0.685  10.959  13960  Z= 0.371
  Chirality :  0.044   0.128   1412
  Planarity :  0.005   0.033   1780
  Dihedral  : 19.409  88.583   3712
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 27.64 %
    Favored  : 68.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.36 %
    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 aren not related in a simple way.
  whole: -1.10 (0.23), residues: 1116
  helix:  0.19 (0.28), residues: 316
  sheet: -0.19 (0.58), residues: 64
  loop : -1.26 (0.21), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 190 
 TYR   0.021   0.001   TYR B 472 
 PHE   0.003   0.001   PHE B 566 
 TRP   0.021   0.002   TRP B 568 
 HIS   0.003   0.001   HIS C 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (10316)
  covalent geometry    : angle       0.68507 (13960)
  hydrogen bonds       : bond        0.21109 (  296)
  hydrogen bonds       : angle       8.38449 (  780)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 204
  time to evaluate  : 0.380 
Fit side-chains
  outliers start: 41
  outliers final: 28
  residues processed: 236
  average time/residue: 0.5938
  time to fit residues: 148.3823
Evaluate side-chains
  214 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 186
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  192 SER
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain A residue  476 LYS
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  500 CYS
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  192 SER
Chi-restraints excluded: chain B residue  368 ASP
Chi-restraints excluded: chain B residue  476 LYS
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  500 CYS
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue  165 SER
Chi-restraints excluded: chain C residue  192 SER
Chi-restraints excluded: chain C residue  368 ASP
Chi-restraints excluded: chain C residue  476 LYS
Chi-restraints excluded: chain C residue  478 VAL
Chi-restraints excluded: chain C residue  500 CYS
Chi-restraints excluded: chain D residue   24 LEU
Chi-restraints excluded: chain D residue  165 SER
Chi-restraints excluded: chain D residue  192 SER
Chi-restraints excluded: chain D residue  368 ASP
Chi-restraints excluded: chain D residue  476 LYS
Chi-restraints excluded: chain D residue  478 VAL
Chi-restraints excluded: chain D residue  500 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.4980
   chunk 113 optimal weight:    0.0970
   chunk 53 optimal weight:    0.0970
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 117 optimal weight:    2.9990
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 573 GLN
** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 573 GLN
C 381 GLN
** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 381 GLN
** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 573 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.215365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.195391 restraints weight = 8705.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.4050 rms_B_bonded: 0.98
r_work: 0.3784 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3725 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.090  10316  Z= 0.181
  Angle     :  0.692  10.567  13960  Z= 0.358
  Chirality :  0.049   0.238   1412
  Planarity :  0.006   0.075   1780
  Dihedral  :  7.607  55.942   1364
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  6.70 %
    Allowed  : 26.13 %
    Favored  : 67.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

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 aren not related in a simple way.
  whole: -0.76 (0.23), residues: 1116
  helix:  0.47 (0.28), residues: 316
  sheet: -0.13 (0.59), residues: 64
  loop : -1.02 (0.21), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 190 
 TYR   0.015   0.002   TYR B 559 
 PHE   0.005   0.001   PHE B 566 
 TRP   0.017   0.002   TRP A 553 
 HIS   0.005   0.001   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 (10316)
  covalent geometry    : angle       0.69204 (13960)
  hydrogen bonds       : bond        0.05375 (  296)
  hydrogen bonds       : angle       6.09505 (  780)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 189
  time to evaluate  : 0.433 
Fit side-chains
REVERT: A   17 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.5290 (mt-10)
REVERT: B   17 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.5342 (mt-10)
REVERT: B  418 HIS cc_start: 0.5864 (OUTLIER) cc_final: 0.5517 (p-80)
REVERT: B  439 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8708 (mtt-85)
REVERT: C   17 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.5306 (mt-10)
REVERT: C  439 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8703 (mtt-85)
REVERT: D   17 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.5282 (mt-10)
REVERT: D  439 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8703 (mtt-85)
REVERT: D  551 LYS cc_start: 0.7007 (mtpp) cc_final: 0.6665 (mttp)
  outliers start: 71
  outliers final: 26
  residues processed: 237
  average time/residue: 0.6144
  time to fit residues: 153.6672
Evaluate side-chains
  226 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 192
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 GLU
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  500 CYS
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain B residue   17 GLU
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  211 ASP
Chi-restraints excluded: chain B residue  380 LYS
Chi-restraints excluded: chain B residue  418 HIS
Chi-restraints excluded: chain B residue  439 ARG
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  500 CYS
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain C residue   17 GLU
Chi-restraints excluded: chain C residue  165 SER
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  211 ASP
Chi-restraints excluded: chain C residue  380 LYS
Chi-restraints excluded: chain C residue  439 ARG
Chi-restraints excluded: chain C residue  478 VAL
Chi-restraints excluded: chain C residue  500 CYS
Chi-restraints excluded: chain C residue  520 ILE
Chi-restraints excluded: chain D residue   17 GLU
Chi-restraints excluded: chain D residue  165 SER
Chi-restraints excluded: chain D residue  167 LEU
Chi-restraints excluded: chain D residue  211 ASP
Chi-restraints excluded: chain D residue  439 ARG
Chi-restraints excluded: chain D residue  478 VAL
Chi-restraints excluded: chain D residue  500 CYS
Chi-restraints excluded: chain D residue  520 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 69 optimal weight:    6.9990
   chunk 104 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 112 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0970
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 381 GLN
** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 381 GLN
** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 381 GLN
** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.212584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.193719 restraints weight = 8590.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3983 rms_B_bonded: 0.81
r_work: 0.3687 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3630 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10316  Z= 0.168
  Angle     :  0.692   7.540  13960  Z= 0.354
  Chirality :  0.048   0.142   1412
  Planarity :  0.006   0.036   1780
  Dihedral  :  5.720  33.209   1328
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  7.26 %
    Allowed  : 25.09 %
    Favored  : 67.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.36 %
    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 aren not related in a simple way.
  whole: -0.83 (0.23), residues: 1116
  helix:  0.44 (0.28), residues: 320
  sheet:  0.03 (0.60), residues: 64
  loop : -1.10 (0.21), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 473 
 TYR   0.013   0.002   TYR B 559 
 PHE   0.006   0.001   PHE D 566 
 TRP   0.017   0.002   TRP C 553 
 HIS   0.005   0.001   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (10316)
  covalent geometry    : angle       0.69182 (13960)
  hydrogen bonds       : bond        0.05022 (  296)
  hydrogen bonds       : angle       5.60188 (  780)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 206
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A   17 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.5439 (mt-10)
REVERT: A  365 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7020 (mt0)
REVERT: A  420 MET cc_start: 0.7654 (mmm) cc_final: 0.7251 (mmm)
REVERT: A  439 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8708 (mtt-85)
REVERT: B   17 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.5432 (mt-10)
REVERT: B  336 ARG cc_start: 0.6788 (mmt-90) cc_final: 0.6536 (mmm160)
REVERT: B  365 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7067 (mt0)
REVERT: B  418 HIS cc_start: 0.5919 (OUTLIER) cc_final: 0.5659 (p-80)
REVERT: B  420 MET cc_start: 0.7652 (mmm) cc_final: 0.7247 (mmm)
REVERT: B  439 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8728 (mtt-85)
REVERT: C   17 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.5408 (mt-10)
REVERT: C  336 ARG cc_start: 0.6794 (mmt-90) cc_final: 0.6559 (mmm160)
REVERT: C  365 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7046 (mt0)
REVERT: C  420 MET cc_start: 0.7684 (mmm) cc_final: 0.7243 (mmm)
REVERT: C  439 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8749 (mtt-85)
REVERT: D   17 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.5413 (mt-10)
REVERT: D  336 ARG cc_start: 0.6747 (mmt-90) cc_final: 0.6541 (mmm160)
REVERT: D  365 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7080 (mt0)
REVERT: D  420 MET cc_start: 0.7636 (mmm) cc_final: 0.7215 (mmm)
REVERT: D  439 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8719 (mtt-85)
  outliers start: 77
  outliers final: 38
  residues processed: 256
  average time/residue: 0.5783
  time to fit residues: 157.1095
Evaluate side-chains
  249 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 198
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 GLU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  365 GLN
Chi-restraints excluded: chain A residue  439 ARG
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  500 CYS
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain B residue   17 GLU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  193 ASP
Chi-restraints excluded: chain B residue  195 SER
Chi-restraints excluded: chain B residue  206 SER
Chi-restraints excluded: chain B residue  211 ASP
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  365 GLN
Chi-restraints excluded: chain B residue  380 LYS
Chi-restraints excluded: chain B residue  418 HIS
Chi-restraints excluded: chain B residue  439 ARG
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  500 CYS
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain C residue   17 GLU
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  193 ASP
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain C residue  211 ASP
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  365 GLN
Chi-restraints excluded: chain C residue  380 LYS
Chi-restraints excluded: chain C residue  439 ARG
Chi-restraints excluded: chain C residue  478 VAL
Chi-restraints excluded: chain C residue  500 CYS
Chi-restraints excluded: chain C residue  520 ILE
Chi-restraints excluded: chain D residue   17 GLU
Chi-restraints excluded: chain D residue  167 LEU
Chi-restraints excluded: chain D residue  193 ASP
Chi-restraints excluded: chain D residue  195 SER
Chi-restraints excluded: chain D residue  206 SER
Chi-restraints excluded: chain D residue  211 ASP
Chi-restraints excluded: chain D residue  365 GLN
Chi-restraints excluded: chain D residue  439 ARG
Chi-restraints excluded: chain D residue  478 VAL
Chi-restraints excluded: chain D residue  500 CYS
Chi-restraints excluded: chain D residue  520 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 91 optimal weight:    0.7980
   chunk 92 optimal weight:    2.9990
   chunk 105 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 65 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 563 GLN
B 381 GLN
B 563 GLN
C 381 GLN
** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 381 GLN
** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.207410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.195124 restraints weight = 8534.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.4037 rms_B_bonded: 0.44
r_work: 0.3844 rms_B_bonded: 1.53 restraints_weight: 0.5000
r_work: 0.3743 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.2795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038  10316  Z= 0.236
  Angle     :  0.743   6.326  13960  Z= 0.382
  Chirality :  0.051   0.165   1412
  Planarity :  0.006   0.038   1780
  Dihedral  :  6.021  41.760   1324
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  8.30 %
    Allowed  : 25.47 %
    Favored  : 66.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.36 %
    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 aren not related in a simple way.
  whole: -1.06 (0.23), residues: 1116
  helix:  0.06 (0.26), residues: 320
  sheet: -0.14 (0.58), residues: 64
  loop : -1.14 (0.22), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 190 
 TYR   0.014   0.002   TYR B 486 
 PHE   0.010   0.002   PHE C 566 
 TRP   0.020   0.002   TRP C 553 
 HIS   0.006   0.001   HIS C 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 (10316)
  covalent geometry    : angle       0.74254 (13960)
  hydrogen bonds       : bond        0.05734 (  296)
  hydrogen bonds       : angle       5.54157 (  780)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 193
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A   17 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.5269 (mt-10)
REVERT: A  350 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7728 (tm)
REVERT: A  365 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7166 (mt0)
REVERT: A  439 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8625 (mtt-85)
REVERT: A  497 ASP cc_start: 0.8176 (m-30) cc_final: 0.7901 (m-30)
REVERT: B   17 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.5383 (mt-10)
REVERT: B  350 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7701 (tm)
REVERT: B  365 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7178 (mt0)
REVERT: B  418 HIS cc_start: 0.6100 (OUTLIER) cc_final: 0.5747 (p-80)
REVERT: B  420 MET cc_start: 0.7537 (mmm) cc_final: 0.7213 (mmm)
REVERT: B  439 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8635 (mtt-85)
REVERT: C   17 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.5354 (mt-10)
REVERT: C  350 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7733 (tm)
REVERT: C  365 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7171 (mt0)
REVERT: C  439 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8630 (mtt-85)
REVERT: C  497 ASP cc_start: 0.8165 (m-30) cc_final: 0.7877 (m-30)
REVERT: D   17 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.5338 (mt-10)
REVERT: D  350 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7699 (tm)
REVERT: D  365 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7187 (mt0)
REVERT: D  439 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8626 (mtt-85)
REVERT: D  497 ASP cc_start: 0.8178 (m-30) cc_final: 0.7883 (m-30)
REVERT: D  551 LYS cc_start: 0.7111 (mtpp) cc_final: 0.6845 (mttp)
  outliers start: 88
  outliers final: 45
  residues processed: 257
  average time/residue: 0.6299
  time to fit residues: 171.5401
Evaluate side-chains
  243 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 181
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 GLU
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  365 GLN
Chi-restraints excluded: chain A residue  428 ASP
Chi-restraints excluded: chain A residue  439 ARG
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  500 CYS
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain B residue   17 GLU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  193 ASP
Chi-restraints excluded: chain B residue  195 SER
Chi-restraints excluded: chain B residue  211 ASP
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  365 GLN
Chi-restraints excluded: chain B residue  418 HIS
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  439 ARG
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  500 CYS
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain C residue   15 ASP
Chi-restraints excluded: chain C residue   17 GLU
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue  165 SER
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  193 ASP
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  211 ASP
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  350 LEU
Chi-restraints excluded: chain C residue  365 GLN
Chi-restraints excluded: chain C residue  428 ASP
Chi-restraints excluded: chain C residue  439 ARG
Chi-restraints excluded: chain C residue  478 VAL
Chi-restraints excluded: chain C residue  500 CYS
Chi-restraints excluded: chain C residue  520 ILE
Chi-restraints excluded: chain D residue   17 GLU
Chi-restraints excluded: chain D residue   24 LEU
Chi-restraints excluded: chain D residue  165 SER
Chi-restraints excluded: chain D residue  167 LEU
Chi-restraints excluded: chain D residue  193 ASP
Chi-restraints excluded: chain D residue  195 SER
Chi-restraints excluded: chain D residue  211 ASP
Chi-restraints excluded: chain D residue  341 LEU
Chi-restraints excluded: chain D residue  350 LEU
Chi-restraints excluded: chain D residue  365 GLN
Chi-restraints excluded: chain D residue  428 ASP
Chi-restraints excluded: chain D residue  439 ARG
Chi-restraints excluded: chain D residue  478 VAL
Chi-restraints excluded: chain D residue  500 CYS
Chi-restraints excluded: chain D residue  520 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 115 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 381 GLN
** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 381 GLN
** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 381 GLN
** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.209331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.195696 restraints weight = 8478.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.4052 rms_B_bonded: 0.49
r_work: 0.3854 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.3762 rms_B_bonded: 2.96 restraints_weight: 0.2500
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.2688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10316  Z= 0.177
  Angle     :  0.668   6.544  13960  Z= 0.344
  Chirality :  0.049   0.136   1412
  Planarity :  0.005   0.036   1780
  Dihedral  :  5.701  41.564   1324
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  8.11 %
    Allowed  : 25.57 %
    Favored  : 66.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.36 %
    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 aren not related in a simple way.
  whole: -1.00 (0.23), residues: 1116
  helix:  0.22 (0.26), residues: 320
  sheet: -0.24 (0.57), residues: 64
  loop : -1.16 (0.22), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 336 
 TYR   0.011   0.002   TYR D 486 
 PHE   0.007   0.001   PHE A 566 
 TRP   0.021   0.002   TRP D 553 
 HIS   0.005   0.001   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 (10316)
  covalent geometry    : angle       0.66833 (13960)
  hydrogen bonds       : bond        0.04969 (  296)
  hydrogen bonds       : angle       5.31455 (  780)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 193
  time to evaluate  : 0.388 
Fit side-chains
REVERT: A   17 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.5233 (mt-10)
REVERT: A  365 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7123 (mt0)
REVERT: A  420 MET cc_start: 0.7537 (mmm) cc_final: 0.6998 (mmm)
REVERT: A  439 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8625 (mtt-85)
REVERT: B   17 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.5234 (mt-10)
REVERT: B  365 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7127 (mt0)
REVERT: B  418 HIS cc_start: 0.6076 (OUTLIER) cc_final: 0.5678 (p-80)
REVERT: B  420 MET cc_start: 0.7471 (mmm) cc_final: 0.7148 (mmm)
REVERT: B  439 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8634 (mtt-85)
REVERT: C   17 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.5236 (mt-10)
REVERT: C  365 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7112 (mt0)
REVERT: C  439 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8616 (mtt-85)
REVERT: D   17 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.5216 (mt-10)
REVERT: D  365 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7107 (mt0)
REVERT: D  420 MET cc_start: 0.7511 (mmm) cc_final: 0.7004 (mmm)
REVERT: D  439 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8638 (mtt-85)
REVERT: D  537 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7921 (mt-10)
  outliers start: 86
  outliers final: 39
  residues processed: 249
  average time/residue: 0.6715
  time to fit residues: 176.6036
Evaluate side-chains
  243 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 190
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 GLU
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  365 GLN
Chi-restraints excluded: chain A residue  428 ASP
Chi-restraints excluded: chain A residue  439 ARG
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  500 CYS
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain B residue   17 GLU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  195 SER
Chi-restraints excluded: chain B residue  211 ASP
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  352 ARG
Chi-restraints excluded: chain B residue  365 GLN
Chi-restraints excluded: chain B residue  418 HIS
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  439 ARG
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  500 CYS
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain C residue   17 GLU
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue  165 SER
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  211 ASP
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  365 GLN
Chi-restraints excluded: chain C residue  428 ASP
Chi-restraints excluded: chain C residue  439 ARG
Chi-restraints excluded: chain C residue  478 VAL
Chi-restraints excluded: chain C residue  500 CYS
Chi-restraints excluded: chain C residue  520 ILE
Chi-restraints excluded: chain D residue   17 GLU
Chi-restraints excluded: chain D residue   24 LEU
Chi-restraints excluded: chain D residue  165 SER
Chi-restraints excluded: chain D residue  167 LEU
Chi-restraints excluded: chain D residue  211 ASP
Chi-restraints excluded: chain D residue  341 LEU
Chi-restraints excluded: chain D residue  352 ARG
Chi-restraints excluded: chain D residue  365 GLN
Chi-restraints excluded: chain D residue  428 ASP
Chi-restraints excluded: chain D residue  439 ARG
Chi-restraints excluded: chain D residue  478 VAL
Chi-restraints excluded: chain D residue  500 CYS
Chi-restraints excluded: chain D residue  520 ILE
Chi-restraints excluded: chain D residue  537 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 83 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.205426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.190743 restraints weight = 8543.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3999 rms_B_bonded: 0.62
r_work: 0.3745 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3666 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.2873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  10316  Z= 0.226
  Angle     :  0.726   6.874  13960  Z= 0.374
  Chirality :  0.051   0.160   1412
  Planarity :  0.006   0.039   1780
  Dihedral  :  5.987  44.487   1324
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  9.15 %
    Allowed  : 24.81 %
    Favored  : 66.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.36 %
    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 aren not related in a simple way.
  whole: -1.14 (0.23), residues: 1116
  helix:  0.00 (0.26), residues: 320
  sheet: -0.33 (0.57), residues: 64
  loop : -1.19 (0.22), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 190 
 TYR   0.014   0.002   TYR B 486 
 PHE   0.009   0.002   PHE C 566 
 TRP   0.022   0.002   TRP D 553 
 HIS   0.006   0.001   HIS D 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 (10316)
  covalent geometry    : angle       0.72574 (13960)
  hydrogen bonds       : bond        0.05529 (  296)
  hydrogen bonds       : angle       5.43793 (  780)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 97
    poor density    : 187
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A   17 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.5379 (mt-10)
REVERT: A  333 ARG cc_start: 0.5694 (OUTLIER) cc_final: 0.5324 (ptp-170)
REVERT: A  350 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7717 (tm)
REVERT: A  365 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7216 (mt0)
REVERT: A  439 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8652 (mtt-85)
REVERT: A  537 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7967 (mt-10)
REVERT: B   17 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.5394 (mt-10)
REVERT: B  333 ARG cc_start: 0.5693 (OUTLIER) cc_final: 0.5310 (ptp-170)
REVERT: B  350 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7726 (tm)
REVERT: B  365 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7225 (mt0)
REVERT: B  418 HIS cc_start: 0.6136 (OUTLIER) cc_final: 0.5646 (p-80)
REVERT: B  420 MET cc_start: 0.7500 (mmm) cc_final: 0.7170 (mmm)
REVERT: B  439 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8669 (mtt-85)
REVERT: B  537 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7945 (mt-10)
REVERT: C   17 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.5380 (mt-10)
REVERT: C  333 ARG cc_start: 0.5675 (OUTLIER) cc_final: 0.5294 (ptp-170)
REVERT: C  350 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7727 (tm)
REVERT: C  365 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7202 (mt0)
REVERT: C  439 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8646 (mtt-85)
REVERT: C  537 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7968 (mt-10)
REVERT: D   17 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.5339 (mt-10)
REVERT: D  333 ARG cc_start: 0.5686 (OUTLIER) cc_final: 0.5298 (ptp-170)
REVERT: D  350 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7722 (tm)
REVERT: D  365 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7219 (mt0)
REVERT: D  439 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8664 (mtt-85)
REVERT: D  537 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8024 (mt-10)
  outliers start: 97
  outliers final: 49
  residues processed: 258
  average time/residue: 0.6452
  time to fit residues: 176.0676
Evaluate side-chains
  261 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 187
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 GLU
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  352 ARG
Chi-restraints excluded: chain A residue  365 GLN
Chi-restraints excluded: chain A residue  428 ASP
Chi-restraints excluded: chain A residue  439 ARG
Chi-restraints excluded: chain A residue  462 SER
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  500 CYS
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  537 GLU
Chi-restraints excluded: chain B residue   15 ASP
Chi-restraints excluded: chain B residue   17 GLU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  193 ASP
Chi-restraints excluded: chain B residue  211 ASP
Chi-restraints excluded: chain B residue  333 ARG
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  352 ARG
Chi-restraints excluded: chain B residue  365 GLN
Chi-restraints excluded: chain B residue  418 HIS
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  439 ARG
Chi-restraints excluded: chain B residue  462 SER
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  500 CYS
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  537 GLU
Chi-restraints excluded: chain C residue   17 GLU
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue  165 SER
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  193 ASP
Chi-restraints excluded: chain C residue  211 ASP
Chi-restraints excluded: chain C residue  333 ARG
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  350 LEU
Chi-restraints excluded: chain C residue  352 ARG
Chi-restraints excluded: chain C residue  365 GLN
Chi-restraints excluded: chain C residue  428 ASP
Chi-restraints excluded: chain C residue  439 ARG
Chi-restraints excluded: chain C residue  462 SER
Chi-restraints excluded: chain C residue  478 VAL
Chi-restraints excluded: chain C residue  500 CYS
Chi-restraints excluded: chain C residue  520 ILE
Chi-restraints excluded: chain C residue  537 GLU
Chi-restraints excluded: chain D residue   15 ASP
Chi-restraints excluded: chain D residue   17 GLU
Chi-restraints excluded: chain D residue   24 LEU
Chi-restraints excluded: chain D residue  165 SER
Chi-restraints excluded: chain D residue  167 LEU
Chi-restraints excluded: chain D residue  193 ASP
Chi-restraints excluded: chain D residue  211 ASP
Chi-restraints excluded: chain D residue  333 ARG
Chi-restraints excluded: chain D residue  341 LEU
Chi-restraints excluded: chain D residue  350 LEU
Chi-restraints excluded: chain D residue  365 GLN
Chi-restraints excluded: chain D residue  428 ASP
Chi-restraints excluded: chain D residue  439 ARG
Chi-restraints excluded: chain D residue  462 SER
Chi-restraints excluded: chain D residue  478 VAL
Chi-restraints excluded: chain D residue  500 CYS
Chi-restraints excluded: chain D residue  520 ILE
Chi-restraints excluded: chain D residue  537 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 99 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 9 optimal weight:    4.9990
   chunk 22 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 87 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.208342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.196590 restraints weight = 8519.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.4069 rms_B_bonded: 0.46
r_work: 0.3876 rms_B_bonded: 1.51 restraints_weight: 0.5000
r_work: 0.3757 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.2811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  10316  Z= 0.163
  Angle     :  0.647   6.748  13960  Z= 0.333
  Chirality :  0.048   0.134   1412
  Planarity :  0.005   0.037   1780
  Dihedral  :  5.554  40.110   1324
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  6.45 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  8.40 %
    Allowed  : 25.09 %
    Favored  : 66.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.36 %
    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 aren not related in a simple way.
  whole: -0.91 (0.23), residues: 1116
  helix:  0.38 (0.27), residues: 320
  sheet: -0.32 (0.58), residues: 64
  loop : -1.13 (0.22), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 190 
 TYR   0.010   0.002   TYR D 486 
 PHE   0.006   0.001   PHE A 566 
 TRP   0.022   0.002   TRP D 553 
 HIS   0.004   0.001   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (10316)
  covalent geometry    : angle       0.64743 (13960)
  hydrogen bonds       : bond        0.04730 (  296)
  hydrogen bonds       : angle       5.24819 (  780)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 89
    poor density    : 187
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A   17 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.5198 (mt-10)
REVERT: A  333 ARG cc_start: 0.5636 (OUTLIER) cc_final: 0.5276 (ptp-170)
REVERT: A  365 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7124 (mt0)
REVERT: A  439 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8623 (mtt-85)
REVERT: A  537 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7929 (mt-10)
REVERT: B   17 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.5181 (mt-10)
REVERT: B  333 ARG cc_start: 0.5650 (OUTLIER) cc_final: 0.5292 (ptp-170)
REVERT: B  365 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7135 (mt0)
REVERT: B  418 HIS cc_start: 0.5987 (OUTLIER) cc_final: 0.5437 (p-80)
REVERT: B  420 MET cc_start: 0.7472 (mmm) cc_final: 0.7179 (mmm)
REVERT: B  439 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8648 (mtt-85)
REVERT: B  537 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7910 (mt-10)
REVERT: C   17 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.5209 (mt-10)
REVERT: C  333 ARG cc_start: 0.5632 (OUTLIER) cc_final: 0.5277 (ptp-170)
REVERT: C  365 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7129 (mt0)
REVERT: C  439 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8635 (mtt-85)
REVERT: C  537 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7938 (mt-10)
REVERT: D   17 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.5188 (mt-10)
REVERT: D  333 ARG cc_start: 0.5653 (OUTLIER) cc_final: 0.5202 (ptp-170)
REVERT: D  365 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7136 (mt0)
REVERT: D  420 MET cc_start: 0.7558 (mmm) cc_final: 0.7086 (mmm)
REVERT: D  439 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8645 (mtt-85)
REVERT: D  537 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7942 (mt-10)
  outliers start: 89
  outliers final: 47
  residues processed: 252
  average time/residue: 0.6192
  time to fit residues: 165.1344
Evaluate side-chains
  252 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 184
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 GLU
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  352 ARG
Chi-restraints excluded: chain A residue  365 GLN
Chi-restraints excluded: chain A residue  428 ASP
Chi-restraints excluded: chain A residue  439 ARG
Chi-restraints excluded: chain A residue  462 SER
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  500 CYS
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  537 GLU
Chi-restraints excluded: chain B residue   17 GLU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  193 ASP
Chi-restraints excluded: chain B residue  211 ASP
Chi-restraints excluded: chain B residue  333 ARG
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  352 ARG
Chi-restraints excluded: chain B residue  365 GLN
Chi-restraints excluded: chain B residue  418 HIS
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  439 ARG
Chi-restraints excluded: chain B residue  462 SER
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  500 CYS
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  537 GLU
Chi-restraints excluded: chain C residue   17 GLU
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue  165 SER
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  193 ASP
Chi-restraints excluded: chain C residue  211 ASP
Chi-restraints excluded: chain C residue  333 ARG
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  352 ARG
Chi-restraints excluded: chain C residue  365 GLN
Chi-restraints excluded: chain C residue  428 ASP
Chi-restraints excluded: chain C residue  439 ARG
Chi-restraints excluded: chain C residue  462 SER
Chi-restraints excluded: chain C residue  478 VAL
Chi-restraints excluded: chain C residue  500 CYS
Chi-restraints excluded: chain C residue  520 ILE
Chi-restraints excluded: chain C residue  537 GLU
Chi-restraints excluded: chain D residue   17 GLU
Chi-restraints excluded: chain D residue   24 LEU
Chi-restraints excluded: chain D residue  165 SER
Chi-restraints excluded: chain D residue  167 LEU
Chi-restraints excluded: chain D residue  193 ASP
Chi-restraints excluded: chain D residue  211 ASP
Chi-restraints excluded: chain D residue  333 ARG
Chi-restraints excluded: chain D residue  341 LEU
Chi-restraints excluded: chain D residue  352 ARG
Chi-restraints excluded: chain D residue  365 GLN
Chi-restraints excluded: chain D residue  428 ASP
Chi-restraints excluded: chain D residue  439 ARG
Chi-restraints excluded: chain D residue  478 VAL
Chi-restraints excluded: chain D residue  500 CYS
Chi-restraints excluded: chain D residue  520 ILE
Chi-restraints excluded: chain D residue  537 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 116 optimal weight:    3.9990
   chunk 115 optimal weight:    2.9990
   chunk 99 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   chunk 108 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 563 GLN
B 563 GLN
C 563 GLN
D 563 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.204234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.188848 restraints weight = 8463.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3958 rms_B_bonded: 0.69
r_work: 0.3690 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3585 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.3017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042  10316  Z= 0.264
  Angle     :  0.774   7.425  13960  Z= 0.399
  Chirality :  0.053   0.171   1412
  Planarity :  0.006   0.041   1780
  Dihedral  :  6.166  46.691   1324
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  8.40 %
    Allowed  : 25.19 %
    Favored  : 66.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.36 %
    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 aren not related in a simple way.
  whole: -1.20 (0.23), residues: 1116
  helix: -0.14 (0.25), residues: 320
  sheet: -0.29 (0.57), residues: 64
  loop : -1.19 (0.22), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 190 
 TYR   0.018   0.003   TYR D 486 
 PHE   0.011   0.002   PHE A 566 
 TRP   0.022   0.002   TRP D 553 
 HIS   0.007   0.001   HIS B 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00620 (10316)
  covalent geometry    : angle       0.77364 (13960)
  hydrogen bonds       : bond        0.05898 (  296)
  hydrogen bonds       : angle       5.52453 (  780)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 89
    poor density    : 184
  time to evaluate  : 0.424 
Fit side-chains
REVERT: A   17 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.5396 (mt-10)
REVERT: A  202 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7840 (ptt)
REVERT: A  333 ARG cc_start: 0.5608 (OUTLIER) cc_final: 0.5274 (ptp-170)
REVERT: A  350 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7750 (tm)
REVERT: A  365 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7191 (mt0)
REVERT: A  439 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8702 (mtt-85)
REVERT: A  537 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8065 (mt-10)
REVERT: B   17 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.5365 (mt-10)
REVERT: B  202 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7765 (ptt)
REVERT: B  333 ARG cc_start: 0.5605 (OUTLIER) cc_final: 0.5259 (ptp-170)
REVERT: B  350 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7758 (tm)
REVERT: B  365 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7181 (mt0)
REVERT: B  418 HIS cc_start: 0.5999 (OUTLIER) cc_final: 0.5387 (p-80)
REVERT: B  420 MET cc_start: 0.7562 (mmm) cc_final: 0.7238 (mmm)
REVERT: B  439 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8702 (mtt-85)
REVERT: B  537 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8053 (mt-10)
REVERT: C   17 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.5372 (mt-10)
REVERT: C  202 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7801 (ptt)
REVERT: C  333 ARG cc_start: 0.5588 (OUTLIER) cc_final: 0.5249 (ptp-170)
REVERT: C  350 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7762 (tm)
REVERT: C  365 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7209 (mt0)
REVERT: C  439 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8705 (mtt-85)
REVERT: C  537 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8058 (mt-10)
REVERT: C  551 LYS cc_start: 0.7161 (mtpp) cc_final: 0.6793 (mttp)
REVERT: D   17 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.5356 (mt-10)
REVERT: D  202 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7754 (ptt)
REVERT: D  333 ARG cc_start: 0.5627 (OUTLIER) cc_final: 0.5269 (ptp-170)
REVERT: D  350 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7755 (tm)
REVERT: D  365 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7205 (mt0)
REVERT: D  439 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8698 (mtt-85)
REVERT: D  537 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8089 (mt-10)
REVERT: D  551 LYS cc_start: 0.7149 (mtpp) cc_final: 0.6798 (mttp)
  outliers start: 89
  outliers final: 51
  residues processed: 249
  average time/residue: 0.7408
  time to fit residues: 194.4976
Evaluate side-chains
  267 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 187
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 GLU
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  202 MET
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  352 ARG
Chi-restraints excluded: chain A residue  365 GLN
Chi-restraints excluded: chain A residue  428 ASP
Chi-restraints excluded: chain A residue  439 ARG
Chi-restraints excluded: chain A residue  462 SER
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  500 CYS
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  537 GLU
Chi-restraints excluded: chain B residue   15 ASP
Chi-restraints excluded: chain B residue   17 GLU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  193 ASP
Chi-restraints excluded: chain B residue  202 MET
Chi-restraints excluded: chain B residue  211 ASP
Chi-restraints excluded: chain B residue  333 ARG
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  352 ARG
Chi-restraints excluded: chain B residue  365 GLN
Chi-restraints excluded: chain B residue  418 HIS
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  439 ARG
Chi-restraints excluded: chain B residue  462 SER
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  500 CYS
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  537 GLU
Chi-restraints excluded: chain C residue   15 ASP
Chi-restraints excluded: chain C residue   17 GLU
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue  165 SER
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  193 ASP
Chi-restraints excluded: chain C residue  202 MET
Chi-restraints excluded: chain C residue  211 ASP
Chi-restraints excluded: chain C residue  333 ARG
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  350 LEU
Chi-restraints excluded: chain C residue  352 ARG
Chi-restraints excluded: chain C residue  365 GLN
Chi-restraints excluded: chain C residue  428 ASP
Chi-restraints excluded: chain C residue  439 ARG
Chi-restraints excluded: chain C residue  462 SER
Chi-restraints excluded: chain C residue  478 VAL
Chi-restraints excluded: chain C residue  500 CYS
Chi-restraints excluded: chain C residue  520 ILE
Chi-restraints excluded: chain C residue  537 GLU
Chi-restraints excluded: chain D residue   15 ASP
Chi-restraints excluded: chain D residue   17 GLU
Chi-restraints excluded: chain D residue   24 LEU
Chi-restraints excluded: chain D residue  165 SER
Chi-restraints excluded: chain D residue  167 LEU
Chi-restraints excluded: chain D residue  193 ASP
Chi-restraints excluded: chain D residue  202 MET
Chi-restraints excluded: chain D residue  211 ASP
Chi-restraints excluded: chain D residue  333 ARG
Chi-restraints excluded: chain D residue  341 LEU
Chi-restraints excluded: chain D residue  350 LEU
Chi-restraints excluded: chain D residue  352 ARG
Chi-restraints excluded: chain D residue  365 GLN
Chi-restraints excluded: chain D residue  428 ASP
Chi-restraints excluded: chain D residue  439 ARG
Chi-restraints excluded: chain D residue  462 SER
Chi-restraints excluded: chain D residue  478 VAL
Chi-restraints excluded: chain D residue  500 CYS
Chi-restraints excluded: chain D residue  520 ILE
Chi-restraints excluded: chain D residue  537 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 53 optimal weight:    0.0670
   chunk 44 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 99 optimal weight:    0.6980
   chunk 93 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 113 optimal weight:    1.9990
   chunk 105 optimal weight:    0.6980
   chunk 76 optimal weight:    0.1980
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.4518

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

Flipped N/Q/H residues before XYZ refinement:
A 450 HIS
** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 450 HIS
** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 450 HIS
** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 450 HIS
** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.210608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.197569 restraints weight = 8433.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.4065 rms_B_bonded: 0.47
r_work: 0.3887 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3777 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.2785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10316  Z= 0.127
  Angle     :  0.611   6.516  13960  Z= 0.313
  Chirality :  0.046   0.130   1412
  Planarity :  0.005   0.038   1780
  Dihedral  :  5.277  35.651   1324
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  6.42 %
    Allowed  : 27.45 %
    Favored  : 66.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.36 %
    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 aren not related in a simple way.
  whole: -0.88 (0.23), residues: 1116
  helix:  0.50 (0.27), residues: 320
  sheet: -0.27 (0.58), residues: 64
  loop : -1.16 (0.22), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 190 
 TYR   0.009   0.001   TYR C 559 
 PHE   0.006   0.001   PHE D 143 
 TRP   0.021   0.002   TRP B 553 
 HIS   0.003   0.001   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (10316)
  covalent geometry    : angle       0.61069 (13960)
  hydrogen bonds       : bond        0.04076 (  296)
  hydrogen bonds       : angle       5.07169 (  780)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 186
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A  365 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7044 (mt0)
REVERT: A  439 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8604 (mtt-85)
REVERT: B  365 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7023 (mt0)
REVERT: B  418 HIS cc_start: 0.5829 (OUTLIER) cc_final: 0.5210 (p-80)
REVERT: B  420 MET cc_start: 0.7401 (mmm) cc_final: 0.7129 (mmm)
REVERT: C  365 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7047 (mt0)
REVERT: D  365 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7050 (mt0)
REVERT: D  537 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7870 (mt-10)
  outliers start: 68
  outliers final: 32
  residues processed: 233
  average time/residue: 0.5688
  time to fit residues: 140.7771
Evaluate side-chains
  221 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 182
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  352 ARG
Chi-restraints excluded: chain A residue  365 GLN
Chi-restraints excluded: chain A residue  428 ASP
Chi-restraints excluded: chain A residue  439 ARG
Chi-restraints excluded: chain A residue  500 CYS
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  193 ASP
Chi-restraints excluded: chain B residue  211 ASP
Chi-restraints excluded: chain B residue  365 GLN
Chi-restraints excluded: chain B residue  418 HIS
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  500 CYS
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain C residue  165 SER
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  193 ASP
Chi-restraints excluded: chain C residue  211 ASP
Chi-restraints excluded: chain C residue  352 ARG
Chi-restraints excluded: chain C residue  365 GLN
Chi-restraints excluded: chain C residue  380 LYS
Chi-restraints excluded: chain C residue  428 ASP
Chi-restraints excluded: chain C residue  500 CYS
Chi-restraints excluded: chain C residue  520 ILE
Chi-restraints excluded: chain D residue  165 SER
Chi-restraints excluded: chain D residue  167 LEU
Chi-restraints excluded: chain D residue  193 ASP
Chi-restraints excluded: chain D residue  211 ASP
Chi-restraints excluded: chain D residue  352 ARG
Chi-restraints excluded: chain D residue  365 GLN
Chi-restraints excluded: chain D residue  462 SER
Chi-restraints excluded: chain D residue  500 CYS
Chi-restraints excluded: chain D residue  520 ILE
Chi-restraints excluded: chain D residue  537 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 106 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 117 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   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 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.207304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.194387 restraints weight = 8417.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.4028 rms_B_bonded: 0.45
r_work: 0.3852 rms_B_bonded: 1.45 restraints_weight: 0.5000
r_work: 0.3732 rms_B_bonded: 3.01 restraints_weight: 0.2500
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.2950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034  10316  Z= 0.202
  Angle     :  0.703   6.947  13960  Z= 0.361
  Chirality :  0.050   0.153   1412
  Planarity :  0.006   0.039   1780
  Dihedral  :  5.380  35.530   1320
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.80 %
    Favored  : 92.20 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 28.96 %
    Favored  : 66.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.36 %
    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 aren not related in a simple way.
  whole: -0.96 (0.23), residues: 1116
  helix:  0.35 (0.27), residues: 320
  sheet: -0.27 (0.57), residues: 64
  loop : -1.18 (0.22), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 336 
 TYR   0.013   0.002   TYR D 486 
 PHE   0.008   0.002   PHE A 566 
 TRP   0.022   0.002   TRP B 553 
 HIS   0.006   0.001   HIS C 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 (10316)
  covalent geometry    : angle       0.70313 (13960)
  hydrogen bonds       : bond        0.05148 (  296)
  hydrogen bonds       : angle       5.29832 (  780)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 177
  time to evaluate  : 0.361 
Fit side-chains
REVERT: A  439 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8644 (mtt-85)
REVERT: A  537 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7978 (mt-10)
REVERT: B  365 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7147 (mt0)
REVERT: B  418 HIS cc_start: 0.5969 (OUTLIER) cc_final: 0.5248 (p-80)
REVERT: B  420 MET cc_start: 0.7503 (mmm) cc_final: 0.7197 (mmm)
REVERT: B  439 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8627 (mtt-85)
REVERT: B  537 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7947 (mt-10)
REVERT: C  333 ARG cc_start: 0.5595 (OUTLIER) cc_final: 0.5248 (ptp-170)
REVERT: C  537 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7970 (mt-10)
REVERT: C  551 LYS cc_start: 0.7181 (mtpp) cc_final: 0.6867 (mttp)
REVERT: D  333 ARG cc_start: 0.5602 (OUTLIER) cc_final: 0.5258 (ptp-170)
REVERT: D  537 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7979 (mt-10)
REVERT: D  551 LYS cc_start: 0.7170 (mtpp) cc_final: 0.6870 (mttp)
  outliers start: 46
  outliers final: 30
  residues processed: 207
  average time/residue: 0.6320
  time to fit residues: 138.1722
Evaluate side-chains
  217 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 177
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  352 ARG
Chi-restraints excluded: chain A residue  428 ASP
Chi-restraints excluded: chain A residue  439 ARG
Chi-restraints excluded: chain A residue  500 CYS
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  537 GLU
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  193 ASP
Chi-restraints excluded: chain B residue  211 ASP
Chi-restraints excluded: chain B residue  365 GLN
Chi-restraints excluded: chain B residue  418 HIS
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  439 ARG
Chi-restraints excluded: chain B residue  500 CYS
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  537 GLU
Chi-restraints excluded: chain C residue  165 SER
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  193 ASP
Chi-restraints excluded: chain C residue  211 ASP
Chi-restraints excluded: chain C residue  333 ARG
Chi-restraints excluded: chain C residue  352 ARG
Chi-restraints excluded: chain C residue  428 ASP
Chi-restraints excluded: chain C residue  500 CYS
Chi-restraints excluded: chain C residue  520 ILE
Chi-restraints excluded: chain C residue  537 GLU
Chi-restraints excluded: chain D residue  165 SER
Chi-restraints excluded: chain D residue  167 LEU
Chi-restraints excluded: chain D residue  193 ASP
Chi-restraints excluded: chain D residue  211 ASP
Chi-restraints excluded: chain D residue  333 ARG
Chi-restraints excluded: chain D residue  462 SER
Chi-restraints excluded: chain D residue  500 CYS
Chi-restraints excluded: chain D residue  520 ILE
Chi-restraints excluded: chain D residue  537 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 92 optimal weight:    0.0970
   chunk 103 optimal weight:    1.9990
   chunk 107 optimal weight:    0.1980
   chunk 93 optimal weight:    0.9980
   chunk 11 optimal weight:    4.9990
   chunk 84 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 97 optimal weight:    2.9990
   chunk 99 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.209072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.192624 restraints weight = 8443.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3980 rms_B_bonded: 0.67
r_work: 0.3678 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3521 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10316  Z= 0.148
  Angle     :  0.642   6.810  13960  Z= 0.329
  Chirality :  0.047   0.132   1412
  Planarity :  0.005   0.036   1780
  Dihedral  :  5.042  28.994   1320
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 29.81 %
    Favored  : 66.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.36 %
    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 aren not related in a simple way.
  whole: -0.88 (0.23), residues: 1116
  helix:  0.53 (0.27), residues: 320
  sheet: -0.21 (0.57), residues: 64
  loop : -1.19 (0.22), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 336 
 TYR   0.009   0.002   TYR D 486 
 PHE   0.006   0.001   PHE C 566 
 TRP   0.022   0.002   TRP D 553 
 HIS   0.004   0.001   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (10316)
  covalent geometry    : angle       0.64170 (13960)
  hydrogen bonds       : bond        0.04401 (  296)
  hydrogen bonds       : angle       5.14613 (  780)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3746.80 seconds
wall clock time: 64 minutes 24.12 seconds (3864.12 seconds total)