Starting phenix.real_space_refine
on Sat Nov 16 00:33:00 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7y_18244/11_2024/8q7y_18244.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7y_18244/11_2024/8q7y_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 {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7y_18244/11_2024/8q7y_18244.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7y_18244/11_2024/8q7y_18244.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7y_18244/11_2024/8q7y_18244.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7y_18244/11_2024/8q7y_18244.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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:
    C, B, D
  Time building chain proxies: 6.07, per 1000 atoms: 0.61
  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: 2.46
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 1.53
  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: 3.17

  Time building geometry restraints manager: 2.82 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: 0.00
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:             6.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.750
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   44.650
-------------------------------------------------------------------------------
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= 0.188
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.021   0.002   TRP B 568 
 HIS   0.003   0.001   HIS C 357 
 PHE   0.003   0.001   PHE B 566 
 TYR   0.021   0.001   TYR B 472 
 ARG   0.007   0.001   ARG B 190 

*********************** 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  : 1.141 
Fit side-chains
  outliers start: 41
  outliers final: 28
  residues processed: 236
  average time/residue: 1.5461
  time to fit residues: 386.7554
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  : 1.131 
-------------------------------------------------------------------------------
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 101 optimal weight:    5.9990
   chunk 90 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 61 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 70 optimal weight:    0.7980
   chunk 108 optimal weight:    0.8980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.1980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.088  10316  Z= 0.316
  Angle     :  0.774  12.292  13960  Z= 0.400
  Chirality :  0.052   0.252   1412
  Planarity :  0.007   0.077   1780
  Dihedral  :  8.510  58.228   1364
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  7.83 %
    Allowed  : 25.47 %
    Favored  : 66.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.23), residues: 1116
  helix:  0.35 (0.28), residues: 316
  sheet: -0.05 (0.60), residues: 64
  loop : -1.09 (0.21), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 553 
 HIS   0.006   0.002   HIS D 395 
 PHE   0.008   0.001   PHE C 566 
 TYR   0.015   0.002   TYR B 559 
 ARG   0.005   0.001   ARG C 190 

*********************** 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
  270 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 187
  time to evaluate  : 1.233 
Fit side-chains
REVERT: A   17 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.5364 (mt-10)
REVERT: A  418 HIS cc_start: 0.6028 (OUTLIER) cc_final: 0.5796 (p-80)
REVERT: A  439 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8563 (mtt-85)
REVERT: B   17 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.5368 (mt-10)
REVERT: B  439 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8574 (mtt-85)
REVERT: C   17 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.5357 (mt-10)
REVERT: C  333 ARG cc_start: 0.5652 (OUTLIER) cc_final: 0.5192 (ptp-170)
REVERT: C  439 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8564 (mtt-85)
REVERT: D   17 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.5360 (mt-10)
REVERT: D  439 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8567 (mtt-85)
REVERT: D  551 LYS cc_start: 0.7176 (mtpp) cc_final: 0.6874 (mttp)
  outliers start: 83
  outliers final: 32
  residues processed: 248
  average time/residue: 1.5365
  time to fit residues: 403.1539
Evaluate side-chains
  216 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 174
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
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  192 SER
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  418 HIS
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  165 SER
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  192 SER
Chi-restraints excluded: chain B residue  195 SER
Chi-restraints excluded: chain B residue  211 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  165 SER
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  192 SER
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  211 ASP
Chi-restraints excluded: chain C residue  333 ARG
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  192 SER
Chi-restraints excluded: chain D residue  195 SER
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 60 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9980
   chunk 30 optimal weight:    0.4980
   chunk 109 optimal weight:    1.9990
   chunk 117 optimal weight:    0.8980
   chunk 97 optimal weight:    5.9990
   chunk 108 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 87 optimal weight:    0.2980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 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: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.2294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10316  Z= 0.278
  Angle     :  0.706   7.741  13960  Z= 0.362
  Chirality :  0.048   0.147   1412
  Planarity :  0.006   0.037   1780
  Dihedral  :  6.725  58.018   1332
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  7.74 %
    Allowed  : 24.53 %
    Favored  : 67.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.23), residues: 1116
  helix:  0.31 (0.28), residues: 320
  sheet: -0.00 (0.59), residues: 64
  loop : -1.12 (0.21), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D 553 
 HIS   0.005   0.001   HIS A 395 
 PHE   0.007   0.001   PHE A 566 
 TYR   0.013   0.002   TYR B 559 
 ARG   0.007   0.001   ARG D 473 

*********************** 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
  269 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 187
  time to evaluate  : 1.114 
Fit side-chains
REVERT: A   17 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.5352 (mt-10)
REVERT: A  365 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.6973 (mt0)
REVERT: A  418 HIS cc_start: 0.5883 (OUTLIER) cc_final: 0.5671 (p-80)
REVERT: A  420 MET cc_start: 0.7377 (mmm) cc_final: 0.6954 (mmm)
REVERT: A  439 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8595 (mtt-85)
REVERT: A  537 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8106 (mp0)
REVERT: B   17 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.5353 (mt-10)
REVERT: B  365 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.6957 (mt0)
REVERT: B  418 HIS cc_start: 0.6024 (OUTLIER) cc_final: 0.5681 (p-80)
REVERT: B  420 MET cc_start: 0.7344 (mmm) cc_final: 0.6920 (mmm)
REVERT: B  439 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8593 (mtt-85)
REVERT: B  537 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8107 (mp0)
REVERT: C   17 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.5347 (mt-10)
REVERT: C  333 ARG cc_start: 0.5654 (OUTLIER) cc_final: 0.5259 (ptp-170)
REVERT: C  365 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.6983 (mt0)
REVERT: C  418 HIS cc_start: 0.6009 (OUTLIER) cc_final: 0.5677 (p-80)
REVERT: C  420 MET cc_start: 0.7413 (mmm) cc_final: 0.6980 (mmm)
REVERT: C  439 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8592 (mtt-85)
REVERT: C  537 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8093 (mp0)
REVERT: D   17 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.5351 (mt-10)
REVERT: D  365 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.6991 (mt0)
REVERT: D  418 HIS cc_start: 0.5987 (OUTLIER) cc_final: 0.5654 (p-80)
REVERT: D  420 MET cc_start: 0.7428 (mmm) cc_final: 0.6985 (mmm)
REVERT: D  439 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8590 (mtt-85)
REVERT: D  537 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8095 (mp0)
  outliers start: 82
  outliers final: 43
  residues processed: 249
  average time/residue: 1.5023
  time to fit residues: 396.3177
Evaluate side-chains
  247 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 187
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
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  192 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  418 HIS
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  192 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  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  192 SER
Chi-restraints excluded: chain C residue  206 SER
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  365 GLN
Chi-restraints excluded: chain C residue  418 HIS
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  192 SER
Chi-restraints excluded: chain D residue  211 ASP
Chi-restraints excluded: chain D residue  341 LEU
Chi-restraints excluded: chain D residue  365 GLN
Chi-restraints excluded: chain D residue  418 HIS
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 107 optimal weight:    3.9990
   chunk 82 optimal weight:    0.7980
   chunk 56 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 109 optimal weight:    0.6980
   chunk 115 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   chunk 103 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0050
   overall best weight:    0.6394

-------------------------------------------------------------------------------
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 381 GLN
** 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: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.2346

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= 0.221
  Angle     :  0.624   6.615  13960  Z= 0.319
  Chirality :  0.047   0.133   1412
  Planarity :  0.005   0.034   1780
  Dihedral  :  5.682  32.083   1332
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  7.08 %
    Allowed  : 25.66 %
    Favored  : 67.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.23), residues: 1116
  helix:  0.49 (0.27), residues: 320
  sheet: -0.29 (0.57), residues: 64
  loop : -1.14 (0.21), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D 553 
 HIS   0.004   0.001   HIS A 395 
 PHE   0.005   0.001   PHE A 566 
 TYR   0.012   0.002   TYR D 559 
 ARG   0.007   0.001   ARG C 336 

*********************** 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
  269 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 194
  time to evaluate  : 1.046 
Fit side-chains
REVERT: A   17 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.5242 (mt-10)
REVERT: A  365 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.6849 (mt0)
REVERT: A  420 MET cc_start: 0.7315 (mmm) cc_final: 0.6906 (mmm)
REVERT: A  439 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8586 (mtt-85)
REVERT: A  537 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8063 (mp0)
REVERT: B   17 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.5251 (mt-10)
REVERT: B  365 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.6842 (mt0)
REVERT: B  418 HIS cc_start: 0.5952 (OUTLIER) cc_final: 0.5583 (p-80)
REVERT: B  420 MET cc_start: 0.7323 (mmm) cc_final: 0.6902 (mmm)
REVERT: B  439 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8580 (mtt-85)
REVERT: B  537 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8064 (mp0)
REVERT: C   17 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.5254 (mt-10)
REVERT: C  333 ARG cc_start: 0.5674 (OUTLIER) cc_final: 0.5275 (ptp-170)
REVERT: C  365 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.6835 (mt0)
REVERT: C  418 HIS cc_start: 0.5951 (OUTLIER) cc_final: 0.5572 (p-80)
REVERT: C  420 MET cc_start: 0.7323 (mmm) cc_final: 0.6899 (mmm)
REVERT: C  439 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8581 (mtt-85)
REVERT: D   17 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.5250 (mt-10)
REVERT: D  365 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.6839 (mt0)
REVERT: D  418 HIS cc_start: 0.5954 (OUTLIER) cc_final: 0.5518 (p-80)
REVERT: D  420 MET cc_start: 0.7350 (mmm) cc_final: 0.6926 (mmm)
REVERT: D  439 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8585 (mtt-85)
REVERT: D  537 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8062 (mp0)
  outliers start: 75
  outliers final: 30
  residues processed: 246
  average time/residue: 1.5364
  time to fit residues: 400.0623
Evaluate side-chains
  239 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 190
  time to evaluate  : 1.171 
-------------------------------------------------------------------------------
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  167 LEU
Chi-restraints excluded: chain A residue  193 ASP
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  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  167 LEU
Chi-restraints excluded: chain B residue  193 ASP
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  418 HIS
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   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  206 SER
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  365 GLN
Chi-restraints excluded: chain C residue  418 HIS
Chi-restraints excluded: chain C residue  439 ARG
Chi-restraints excluded: chain C residue  462 SER
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  167 LEU
Chi-restraints excluded: chain D residue  193 ASP
Chi-restraints excluded: chain D residue  211 ASP
Chi-restraints excluded: chain D residue  341 LEU
Chi-restraints excluded: chain D residue  365 GLN
Chi-restraints excluded: chain D residue  418 HIS
Chi-restraints excluded: chain D residue  439 ARG
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 86 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 104 optimal weight:    0.2980
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2499

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= 0.251
  Angle     :  0.645   6.329  13960  Z= 0.332
  Chirality :  0.048   0.143   1412
  Planarity :  0.005   0.035   1780
  Dihedral  :  5.145  31.410   1320
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  7.74 %
    Allowed  : 25.28 %
    Favored  : 66.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.23), residues: 1116
  helix:  0.34 (0.27), residues: 320
  sheet: -0.35 (0.57), residues: 64
  loop : -1.15 (0.22), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP D 553 
 HIS   0.005   0.001   HIS A 395 
 PHE   0.006   0.001   PHE C 566 
 TYR   0.011   0.002   TYR D 559 
 ARG   0.006   0.001   ARG A 190 

*********************** 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
  263 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 181
  time to evaluate  : 1.310 
Fit side-chains
REVERT: A   17 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.5294 (mt-10)
REVERT: A  365 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.6936 (mt0)
REVERT: A  418 HIS cc_start: 0.5984 (OUTLIER) cc_final: 0.5403 (p-80)
REVERT: A  420 MET cc_start: 0.7305 (mmm) cc_final: 0.6922 (mmm)
REVERT: A  439 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8591 (mtt-85)
REVERT: B   17 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.5298 (mt-10)
REVERT: B  365 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.6933 (mt0)
REVERT: B  418 HIS cc_start: 0.5969 (OUTLIER) cc_final: 0.5451 (p-80)
REVERT: B  420 MET cc_start: 0.7298 (mmm) cc_final: 0.6891 (mmm)
REVERT: B  439 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8604 (mtt-85)
REVERT: C   17 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.5293 (mt-10)
REVERT: C  333 ARG cc_start: 0.5612 (OUTLIER) cc_final: 0.5202 (ptp-170)
REVERT: C  365 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.6924 (mt0)
REVERT: C  418 HIS cc_start: 0.5956 (OUTLIER) cc_final: 0.5418 (p-80)
REVERT: C  420 MET cc_start: 0.7348 (mmm) cc_final: 0.6922 (mmm)
REVERT: C  439 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8608 (mtt-85)
REVERT: C  537 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8167 (mt-10)
REVERT: D   17 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.5296 (mt-10)
REVERT: D  365 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.6936 (mt0)
REVERT: D  418 HIS cc_start: 0.5960 (OUTLIER) cc_final: 0.5499 (p-80)
REVERT: D  420 MET cc_start: 0.7355 (mmm) cc_final: 0.6942 (mmm)
REVERT: D  439 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8607 (mtt-85)
  outliers start: 82
  outliers final: 42
  residues processed: 237
  average time/residue: 1.5115
  time to fit residues: 380.0955
Evaluate side-chains
  247 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 187
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
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  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  418 HIS
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  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  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  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  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  206 SER
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  365 GLN
Chi-restraints excluded: chain C residue  418 HIS
Chi-restraints excluded: chain C residue  428 ASP
Chi-restraints excluded: chain C residue  439 ARG
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  206 SER
Chi-restraints excluded: chain D residue  211 ASP
Chi-restraints excluded: chain D residue  341 LEU
Chi-restraints excluded: chain D residue  365 GLN
Chi-restraints excluded: chain D residue  418 HIS
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  500 CYS
Chi-restraints excluded: chain D residue  520 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 104 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 116 optimal weight:    1.9990
   chunk 96 optimal weight:    4.9990
   chunk 53 optimal weight:    0.5980
   chunk 9 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 60 optimal weight:    4.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
A 563 GLN
B 563 GLN
** 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: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.2806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040  10316  Z= 0.383
  Angle     :  0.756   6.958  13960  Z= 0.390
  Chirality :  0.052   0.172   1412
  Planarity :  0.006   0.040   1780
  Dihedral  :  5.696  40.389   1320
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  9.15 %
    Allowed  : 23.49 %
    Favored  : 67.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.23), residues: 1116
  helix: -0.06 (0.26), residues: 320
  sheet: -0.33 (0.57), residues: 64
  loop : -1.16 (0.22), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D 553 
 HIS   0.006   0.001   HIS D 395 
 PHE   0.010   0.002   PHE A 566 
 TYR   0.015   0.003   TYR A 486 
 ARG   0.004   0.001   ARG A 388 

*********************** 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
  288 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 97
    poor density    : 191
  time to evaluate  : 1.147 
Fit side-chains
REVERT: A   17 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.5346 (mt-10)
REVERT: A  350 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7775 (tm)
REVERT: A  365 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7137 (mt0)
REVERT: A  418 HIS cc_start: 0.6018 (OUTLIER) cc_final: 0.5365 (p-80)
REVERT: A  420 MET cc_start: 0.7363 (mmm) cc_final: 0.7001 (mmm)
REVERT: A  439 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8603 (mtt-85)
REVERT: A  537 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8130 (mt-10)
REVERT: B   17 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.5371 (mt-10)
REVERT: B  350 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7773 (tm)
REVERT: B  365 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7131 (mt0)
REVERT: B  418 HIS cc_start: 0.5959 (OUTLIER) cc_final: 0.5291 (p-80)
REVERT: B  420 MET cc_start: 0.7388 (mmm) cc_final: 0.7011 (mmm)
REVERT: B  439 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8603 (mtt-85)
REVERT: B  537 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8129 (mt-10)
REVERT: C   17 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.5363 (mt-10)
REVERT: C  202 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7553 (ptt)
REVERT: C  333 ARG cc_start: 0.5563 (OUTLIER) cc_final: 0.5175 (ptp-170)
REVERT: C  350 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7777 (tm)
REVERT: C  365 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7106 (mt0)
REVERT: C  418 HIS cc_start: 0.5939 (OUTLIER) cc_final: 0.5302 (p-80)
REVERT: C  420 MET cc_start: 0.7395 (mmm) cc_final: 0.7001 (mmm)
REVERT: C  439 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8604 (mtt-85)
REVERT: C  537 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8132 (mt-10)
REVERT: C  551 LYS cc_start: 0.7390 (mtpp) cc_final: 0.7059 (mttp)
REVERT: D   17 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.5367 (mt-10)
REVERT: D  202 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7541 (ptt)
REVERT: D  350 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7770 (tm)
REVERT: D  365 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7114 (mt0)
REVERT: D  418 HIS cc_start: 0.5950 (OUTLIER) cc_final: 0.5284 (p-80)
REVERT: D  420 MET cc_start: 0.7397 (mmm) cc_final: 0.7001 (mmm)
REVERT: D  439 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8604 (mtt-85)
REVERT: D  537 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8130 (mt-10)
REVERT: D  551 LYS cc_start: 0.7377 (mtpp) cc_final: 0.7043 (mttp)
  outliers start: 97
  outliers final: 52
  residues processed: 265
  average time/residue: 1.5235
  time to fit residues: 427.7068
Evaluate side-chains
  264 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 185
  time to evaluate  : 1.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ASP
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  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  418 HIS
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  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  380 LYS
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  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  418 HIS
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  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  418 HIS
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 111 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 84 optimal weight:    0.0980
   chunk 65 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9980
   chunk 115 optimal weight:    1.9990
   chunk 72 optimal weight:    0.0980
   chunk 70 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 450 HIS
** 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: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.2632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10316  Z= 0.206
  Angle     :  0.611   6.539  13960  Z= 0.314
  Chirality :  0.047   0.130   1412
  Planarity :  0.005   0.037   1780
  Dihedral  :  5.065  31.083   1320
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  9.53 %
    Allowed  : 24.15 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.24), residues: 1116
  helix:  0.43 (0.27), residues: 320
  sheet: -0.37 (0.57), residues: 64
  loop : -1.06 (0.22), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP D 553 
 HIS   0.003   0.001   HIS A 395 
 PHE   0.006   0.001   PHE A 143 
 TYR   0.008   0.001   TYR B 161 
 ARG   0.004   0.001   ARG C 190 

*********************** 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
  281 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 101
    poor density    : 180
  time to evaluate  : 1.079 
Fit side-chains
REVERT: A   17 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.5235 (mt-10)
REVERT: A  333 ARG cc_start: 0.5667 (OUTLIER) cc_final: 0.5193 (ptp-170)
REVERT: A  365 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.6999 (mt0)
REVERT: A  418 HIS cc_start: 0.5874 (OUTLIER) cc_final: 0.5199 (p-80)
REVERT: A  420 MET cc_start: 0.7262 (mmm) cc_final: 0.6917 (mmm)
REVERT: A  439 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8616 (mtt-85)
REVERT: A  537 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7988 (mt-10)
REVERT: B   17 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.5242 (mt-10)
REVERT: B  202 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7346 (ptt)
REVERT: B  333 ARG cc_start: 0.5695 (OUTLIER) cc_final: 0.5236 (ptp-170)
REVERT: B  365 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.6895 (mt0)
REVERT: B  418 HIS cc_start: 0.5954 (OUTLIER) cc_final: 0.5278 (p-80)
REVERT: B  420 MET cc_start: 0.7279 (mmm) cc_final: 0.6905 (mmm)
REVERT: B  439 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8607 (mtt-85)
REVERT: B  537 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8020 (mt-10)
REVERT: C  193 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7161 (t70)
REVERT: C  202 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7345 (ptt)
REVERT: C  333 ARG cc_start: 0.5612 (OUTLIER) cc_final: 0.5248 (ptp-170)
REVERT: C  365 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.6899 (mt0)
REVERT: C  418 HIS cc_start: 0.5936 (OUTLIER) cc_final: 0.5222 (p-80)
REVERT: C  420 MET cc_start: 0.7298 (mmm) cc_final: 0.6922 (mmm)
REVERT: C  439 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8603 (mtt-85)
REVERT: C  537 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8088 (mt-10)
REVERT: D   17 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.5254 (mt-10)
REVERT: D  202 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7331 (ptt)
REVERT: D  333 ARG cc_start: 0.5675 (OUTLIER) cc_final: 0.5220 (ptp-170)
REVERT: D  365 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.6899 (mt0)
REVERT: D  418 HIS cc_start: 0.5871 (OUTLIER) cc_final: 0.5230 (p-80)
REVERT: D  420 MET cc_start: 0.7299 (mmm) cc_final: 0.6918 (mmm)
REVERT: D  439 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8609 (mtt-85)
REVERT: D  537 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8034 (mt-10)
  outliers start: 101
  outliers final: 44
  residues processed: 254
  average time/residue: 1.5618
  time to fit residues: 419.2858
Evaluate side-chains
  239 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 168
  time to evaluate  : 1.167 
-------------------------------------------------------------------------------
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  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  418 HIS
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  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  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   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  352 ARG
Chi-restraints excluded: chain C residue  365 GLN
Chi-restraints excluded: chain C residue  418 HIS
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  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  352 ARG
Chi-restraints excluded: chain D residue  365 GLN
Chi-restraints excluded: chain D residue  418 HIS
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 69 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.051  10316  Z= 0.491
  Angle     :  0.835   7.868  13960  Z= 0.433
  Chirality :  0.056   0.197   1412
  Planarity :  0.007   0.044   1780
  Dihedral  :  6.073  46.914   1320
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.80 %
    Favored  : 92.20 %
  Rotamer:
    Outliers :  8.49 %
    Allowed  : 25.75 %
    Favored  : 65.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.23), residues: 1116
  helix: -0.38 (0.25), residues: 320
  sheet: -0.41 (0.56), residues: 64
  loop : -1.19 (0.22), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP A 553 
 HIS   0.008   0.002   HIS C 395 
 PHE   0.013   0.002   PHE A 566 
 TYR   0.020   0.003   TYR C 486 
 ARG   0.004   0.001   ARG D 190 

*********************** 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: 90
    poor density    : 183
  time to evaluate  : 1.175 
Fit side-chains
REVERT: A   17 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.5357 (mt-10)
REVERT: A  333 ARG cc_start: 0.5624 (OUTLIER) cc_final: 0.5254 (ptp-170)
REVERT: A  350 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7839 (tm)
REVERT: A  365 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7216 (mt0)
REVERT: A  403 ASP cc_start: 0.8092 (p0) cc_final: 0.7866 (p0)
REVERT: A  420 MET cc_start: 0.7376 (mmm) cc_final: 0.6986 (mmm)
REVERT: A  439 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8651 (mtt-85)
REVERT: A  537 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8094 (mt-10)
REVERT: A  551 LYS cc_start: 0.7325 (mtpp) cc_final: 0.7009 (mttp)
REVERT: B   17 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.5361 (mt-10)
REVERT: B  202 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7529 (ptt)
REVERT: B  333 ARG cc_start: 0.5624 (OUTLIER) cc_final: 0.5267 (ptp-170)
REVERT: B  350 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7824 (tm)
REVERT: B  365 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7164 (mt0)
REVERT: B  403 ASP cc_start: 0.8116 (p0) cc_final: 0.7874 (p0)
REVERT: B  418 HIS cc_start: 0.5914 (OUTLIER) cc_final: 0.5186 (p-80)
REVERT: B  420 MET cc_start: 0.7394 (mmm) cc_final: 0.7016 (mmm)
REVERT: B  439 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8652 (mtt-85)
REVERT: B  537 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8119 (mt-10)
REVERT: B  551 LYS cc_start: 0.7323 (mtpp) cc_final: 0.7006 (mttp)
REVERT: C   17 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.5271 (mt-10)
REVERT: C  333 ARG cc_start: 0.5601 (OUTLIER) cc_final: 0.5186 (ptp-170)
REVERT: C  350 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7824 (tm)
REVERT: C  365 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7226 (mt0)
REVERT: C  403 ASP cc_start: 0.8088 (p0) cc_final: 0.7854 (p0)
REVERT: C  418 HIS cc_start: 0.5920 (OUTLIER) cc_final: 0.5143 (p-80)
REVERT: C  420 MET cc_start: 0.7389 (mmm) cc_final: 0.7011 (mmm)
REVERT: C  439 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8658 (mtt-85)
REVERT: C  537 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8064 (mt-10)
REVERT: C  551 LYS cc_start: 0.7327 (mtpp) cc_final: 0.7009 (mttp)
REVERT: D   17 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.5367 (mt-10)
REVERT: D  333 ARG cc_start: 0.5624 (OUTLIER) cc_final: 0.5263 (ptp-170)
REVERT: D  350 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7826 (tm)
REVERT: D  365 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7228 (mt0)
REVERT: D  403 ASP cc_start: 0.8094 (p0) cc_final: 0.7866 (p0)
REVERT: D  418 HIS cc_start: 0.5908 (OUTLIER) cc_final: 0.5172 (p-80)
REVERT: D  420 MET cc_start: 0.7400 (mmm) cc_final: 0.7016 (mmm)
REVERT: D  439 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8652 (mtt-85)
REVERT: D  537 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8113 (mt-10)
REVERT: D  551 LYS cc_start: 0.7322 (mtpp) cc_final: 0.7009 (mttp)
  outliers start: 90
  outliers final: 51
  residues processed: 249
  average time/residue: 1.5746
  time to fit residues: 414.3473
Evaluate side-chains
  259 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 180
  time to evaluate  : 1.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ASP
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  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   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  418 HIS
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  352 ARG
Chi-restraints excluded: chain D residue  365 GLN
Chi-restraints excluded: chain D residue  418 HIS
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 110 optimal weight:    0.6980
   chunk 101 optimal weight:    3.9990
   chunk 107 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 84 optimal weight:    0.0980
   chunk 33 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 113 optimal weight:    0.7980
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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
** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.2721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10316  Z= 0.223
  Angle     :  0.635   6.510  13960  Z= 0.327
  Chirality :  0.047   0.133   1412
  Planarity :  0.005   0.038   1780
  Dihedral  :  5.352  38.341   1320
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  7.64 %
    Allowed  : 26.89 %
    Favored  : 65.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.23), residues: 1116
  helix: -0.11 (0.26), residues: 344
  sheet: -0.39 (0.56), residues: 64
  loop : -1.28 (0.22), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D 553 
 HIS   0.004   0.001   HIS A 395 
 PHE   0.007   0.001   PHE A 143 
 TYR   0.009   0.002   TYR D 161 
 ARG   0.004   0.001   ARG C 190 

*********************** 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
  260 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 179
  time to evaluate  : 1.149 
Fit side-chains
REVERT: A   17 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.5145 (mt-10)
REVERT: A  333 ARG cc_start: 0.5693 (OUTLIER) cc_final: 0.5247 (ptp-170)
REVERT: A  365 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7018 (mt0)
REVERT: A  420 MET cc_start: 0.7259 (mmm) cc_final: 0.6935 (mmm)
REVERT: A  439 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8620 (mtt-85)
REVERT: A  537 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8037 (mt-10)
REVERT: B   17 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.5144 (mt-10)
REVERT: B  333 ARG cc_start: 0.5699 (OUTLIER) cc_final: 0.5245 (ptp-170)
REVERT: B  365 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7021 (mt0)
REVERT: B  418 HIS cc_start: 0.6000 (OUTLIER) cc_final: 0.5174 (p-80)
REVERT: B  420 MET cc_start: 0.7288 (mmm) cc_final: 0.6953 (mmm)
REVERT: B  439 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8611 (mtt-85)
REVERT: B  537 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8051 (mt-10)
REVERT: C  193 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7115 (t70)
REVERT: C  333 ARG cc_start: 0.5566 (OUTLIER) cc_final: 0.4940 (ptp-170)
REVERT: C  365 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7038 (mt0)
REVERT: C  418 HIS cc_start: 0.5964 (OUTLIER) cc_final: 0.5182 (p-80)
REVERT: C  420 MET cc_start: 0.7301 (mmm) cc_final: 0.6971 (mmm)
REVERT: C  439 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8608 (mtt-85)
REVERT: C  537 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8090 (mt-10)
REVERT: D   17 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.5148 (mt-10)
REVERT: D  333 ARG cc_start: 0.5696 (OUTLIER) cc_final: 0.5245 (ptp-170)
REVERT: D  365 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7036 (mt0)
REVERT: D  418 HIS cc_start: 0.5991 (OUTLIER) cc_final: 0.5177 (p-80)
REVERT: D  420 MET cc_start: 0.7303 (mmm) cc_final: 0.6964 (mmm)
REVERT: D  439 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8624 (mtt-85)
REVERT: D  537 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8052 (mt-10)
  outliers start: 81
  outliers final: 46
  residues processed: 236
  average time/residue: 1.5242
  time to fit residues: 380.8890
Evaluate side-chains
  240 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 171
  time to evaluate  : 1.238 
-------------------------------------------------------------------------------
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  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   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  418 HIS
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  418 HIS
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 119 optimal weight:    1.9990
   chunk 110 optimal weight:    0.0060
   chunk 95 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   chunk 75 optimal weight:    0.9990
   chunk 101 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.8800

-------------------------------------------------------------------------------
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
** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.2764

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= 0.271
  Angle     :  0.676   6.614  13960  Z= 0.348
  Chirality :  0.049   0.148   1412
  Planarity :  0.005   0.037   1780
  Dihedral  :  5.303  33.168   1320
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  6.60 %
    Allowed  : 27.55 %
    Favored  : 65.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.23), residues: 1116
  helix: -0.05 (0.26), residues: 344
  sheet: -0.39 (0.55), residues: 64
  loop : -1.30 (0.22), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C 553 
 HIS   0.005   0.001   HIS D 395 
 PHE   0.007   0.001   PHE A 209 
 TYR   0.012   0.002   TYR B 486 
 ARG   0.005   0.001   ARG C 336 

********************** 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
  241 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 171
  time to evaluate  : 1.118 
Fit side-chains
REVERT: A   17 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.5275 (mt-10)
REVERT: A  333 ARG cc_start: 0.5680 (OUTLIER) cc_final: 0.5278 (ptp-170)
REVERT: A  365 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7077 (mt0)
REVERT: A  420 MET cc_start: 0.7279 (mmm) cc_final: 0.6915 (mmm)
REVERT: A  439 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8619 (mtt-85)
REVERT: A  537 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8089 (mt-10)
REVERT: B   17 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.5274 (mt-10)
REVERT: B  333 ARG cc_start: 0.5682 (OUTLIER) cc_final: 0.5274 (ptp-170)
REVERT: B  418 HIS cc_start: 0.6039 (OUTLIER) cc_final: 0.5222 (p-80)
REVERT: B  420 MET cc_start: 0.7296 (mmm) cc_final: 0.6929 (mmm)
REVERT: B  439 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8621 (mtt-85)
REVERT: B  537 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8090 (mt-10)
REVERT: C   17 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.5291 (mt-10)
REVERT: C  193 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7135 (t70)
REVERT: C  333 ARG cc_start: 0.5586 (OUTLIER) cc_final: 0.5216 (ptp-170)
REVERT: C  418 HIS cc_start: 0.5996 (OUTLIER) cc_final: 0.5134 (p-80)
REVERT: C  420 MET cc_start: 0.7310 (mmm) cc_final: 0.6944 (mmm)
REVERT: C  439 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8617 (mtt-85)
REVERT: C  537 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8174 (mt-10)
REVERT: C  551 LYS cc_start: 0.7339 (mtpp) cc_final: 0.7022 (mttp)
REVERT: D   17 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.5254 (mt-10)
REVERT: D  193 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7105 (t70)
REVERT: D  333 ARG cc_start: 0.5681 (OUTLIER) cc_final: 0.5273 (ptp-170)
REVERT: D  418 HIS cc_start: 0.6017 (OUTLIER) cc_final: 0.5194 (p-80)
REVERT: D  420 MET cc_start: 0.7304 (mmm) cc_final: 0.6931 (mmm)
REVERT: D  439 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8618 (mtt-85)
REVERT: D  537 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8091 (mt-10)
REVERT: D  551 LYS cc_start: 0.7332 (mtpp) cc_final: 0.7015 (mttp)
  outliers start: 70
  outliers final: 41
  residues processed: 219
  average time/residue: 1.5633
  time to fit residues: 362.9033
Evaluate side-chains
  232 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 169
  time to evaluate  : 1.471 
-------------------------------------------------------------------------------
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  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  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  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  418 HIS
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  418 HIS
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 87 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 95 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 83 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    1.5388

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.4161 r_free = 0.4161 target = 0.204557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.179459 restraints weight = 8355.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3747 rms_B_bonded: 1.56
r_work: 0.3438 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.2924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041  10316  Z= 0.403
  Angle     :  0.779   6.750  13960  Z= 0.404
  Chirality :  0.053   0.178   1412
  Planarity :  0.006   0.041   1780
  Dihedral  :  5.746  39.549   1320
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  7.64 %
    Allowed  : 26.51 %
    Favored  : 65.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.23), residues: 1116
  helix: -0.11 (0.26), residues: 320
  sheet: -0.29 (0.55), residues: 64
  loop : -1.20 (0.22), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP D 553 
 HIS   0.007   0.001   HIS D 395 
 PHE   0.011   0.002   PHE A 566 
 TYR   0.018   0.003   TYR C 486 
 ARG   0.005   0.001   ARG B 190 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5630.70 seconds
wall clock time: 100 minutes 33.21 seconds (6033.21 seconds total)