Starting phenix.real_space_refine
on Tue Mar 11 20:20:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dk8_46946/03_2025/9dk8_46946.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dk8_46946/03_2025/9dk8_46946.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dk8_46946/03_2025/9dk8_46946.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dk8_46946/03_2025/9dk8_46946.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dk8_46946/03_2025/9dk8_46946.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dk8_46946/03_2025/9dk8_46946.cif"
  }
  resolution = 3.3
  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=   0.002 sd=   0.025
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      36      5.16       5
     C    4206      2.51       5
     N    1194      2.21       5
     O    1242      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6678
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "E"
      Number of atoms: 1113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1113
          Classifications: {'peptide': 143}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 135}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 1113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1113
          Classifications: {'peptide': 143}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 135}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "F"
      Number of atoms: 1113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1113
          Classifications: {'peptide': 143}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 135}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 1113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1113
          Classifications: {'peptide': 143}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 135}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 1113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1113
          Classifications: {'peptide': 143}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 135}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 1113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1113
          Classifications: {'peptide': 143}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 135}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 4.71, per 1000 atoms: 0.71
  Number of scatterers: 6678
  At special positions: 0
  Unit cell: (66.825, 62.7, 137.775, 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      36     16.00
     O    1242      8.00
     N    1194      7.00
     C    4206      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: 1.63
  Conformation dependent library (CDL) restraints added in 944.5 milliseconds
  

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1644

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 6 sheets defined
      49.4% alpha, 11.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.68
  Creating SS restraints...
    Processing helix  chain 'E' and resid 405 through 420
      removed outlier: 3.954A  pdb=" N   ALA E 409 " --> pdb=" O   ASP E 405 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   GLY E 420 " --> pdb=" O   LEU E 416 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 439 through 448
    Processing helix  chain 'E' and resid 457 through 461
      removed outlier: 3.985A  pdb=" N   ASP E 461 " --> pdb=" O   SER E 458 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 462 through 479
    Processing helix  chain 'E' and resid 495 through 499
      removed outlier: 3.803A  pdb=" N   LEU E 499 " --> pdb=" O   PRO E 496 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 503 through 508
    Processing helix  chain 'E' and resid 519 through 528
    Processing helix  chain 'B' and resid 405 through 419
      removed outlier: 3.990A  pdb=" N   ALA B 418 " --> pdb=" O   GLU B 414 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   LEU B 419 " --> pdb=" O   LYS B 415 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 426 through 431
      removed outlier: 4.044A  pdb=" N   PHE B 431 " --> pdb=" O   CYS B 428 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 438 through 448
    Processing helix  chain 'B' and resid 462 through 479
    Processing helix  chain 'B' and resid 495 through 499
      removed outlier: 3.604A  pdb=" N   LEU B 499 " --> pdb=" O   PRO B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 500 through 507
      removed outlier: 4.067A  pdb=" N   LEU B 506 " --> pdb=" O   ASP B 502 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   LEU B 507 " --> pdb=" O   THR B 503 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 519 through 528
    Processing helix  chain 'F' and resid 405 through 419
      removed outlier: 3.852A  pdb=" N   ALA F 409 " --> pdb=" O   ASP F 405 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 442 through 448
      removed outlier: 3.595A  pdb=" N   ILE F 446 " --> pdb=" O   LEU F 442 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 457 through 461
      removed outlier: 3.905A  pdb=" N   ASP F 461 " --> pdb=" O   SER F 458 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 462 through 479
      removed outlier: 3.507A  pdb=" N   HIS F 467 " --> pdb=" O   ARG F 463 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 495 through 499
    Processing helix  chain 'F' and resid 500 through 505
    Processing helix  chain 'F' and resid 506 through 508
      No H-bonds generated for 'chain 'F' and resid 506 through 508'
    Processing helix  chain 'F' and resid 519 through 528
    Processing helix  chain 'D' and resid 405 through 419
      removed outlier: 3.542A  pdb=" N   ALA D 409 " --> pdb=" O   ASP D 405 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 426 through 430
    Processing helix  chain 'D' and resid 440 through 448
    Processing helix  chain 'D' and resid 457 through 461
      removed outlier: 4.081A  pdb=" N   ASP D 461 " --> pdb=" O   SER D 458 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 462 through 479
    Processing helix  chain 'D' and resid 495 through 499
      removed outlier: 3.982A  pdb=" N   LEU D 499 " --> pdb=" O   PRO D 496 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 500 through 505
      removed outlier: 3.569A  pdb=" N   SER D 505 " --> pdb=" O   SER D 501 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 506 through 510
      removed outlier: 4.381A  pdb=" N   GLY D 509 " --> pdb=" O   LEU D 506 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 519 through 528
    Processing helix  chain 'A' and resid 405 through 420
      removed outlier: 3.819A  pdb=" N   ALA A 409 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLY A 420 " --> pdb=" O   LEU A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 430
      removed outlier: 3.505A  pdb=" N   ASP A 430 " --> pdb=" O   PHE A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 437 through 448
    Processing helix  chain 'A' and resid 462 through 479
    Processing helix  chain 'A' and resid 500 through 505
    Processing helix  chain 'A' and resid 519 through 528
    Processing helix  chain 'C' and resid 405 through 419
    Processing helix  chain 'C' and resid 441 through 448
    Processing helix  chain 'C' and resid 457 through 461
      removed outlier: 3.954A  pdb=" N   ASP C 461 " --> pdb=" O   SER C 458 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 462 through 479
    Processing helix  chain 'C' and resid 495 through 499
      removed outlier: 4.153A  pdb=" N   LEU C 499 " --> pdb=" O   PRO C 496 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 500 through 505
    Processing helix  chain 'C' and resid 519 through 528
    Processing sheet with id=AA1, first strand: chain 'E' and resid 395 through 400
      removed outlier: 6.618A  pdb=" N   ASN E 396 " --> pdb=" O   PHE E 451 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   ILE E 453 " --> pdb=" O   ASN E 396 " (cutoff:3.500A)
      removed outlier: 6.171A  pdb=" N   VAL E 398 " --> pdb=" O   ILE E 453 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   LEU E 455 " --> pdb=" O   VAL E 398 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   LEU E 400 " --> pdb=" O   LEU E 455 " (cutoff:3.500A)
      removed outlier: 8.208A  pdb=" N   ILE E 487 " --> pdb=" O   ALA E 450 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   ILE E 452 " --> pdb=" O   ILE E 487 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   PHE E 489 " --> pdb=" O   ILE E 452 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   LEU E 454 " --> pdb=" O   PHE E 489 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 395 through 400
      removed outlier: 6.435A  pdb=" N   ASN B 396 " --> pdb=" O   PHE B 451 " (cutoff:3.500A)
      removed outlier: 7.660A  pdb=" N   ILE B 453 " --> pdb=" O   ASN B 396 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   VAL B 398 " --> pdb=" O   ILE B 453 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   LEU B 455 " --> pdb=" O   VAL B 398 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   LEU B 400 " --> pdb=" O   LEU B 455 " (cutoff:3.500A)
      removed outlier: 8.701A  pdb=" N   ILE B 487 " --> pdb=" O   ALA B 450 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   ILE B 452 " --> pdb=" O   ILE B 487 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   PHE B 489 " --> pdb=" O   ILE B 452 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   LEU B 454 " --> pdb=" O   PHE B 489 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'F' and resid 395 through 400
      removed outlier: 6.922A  pdb=" N   ASN F 396 " --> pdb=" O   SER F 449 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 395 through 400
      removed outlier: 6.594A  pdb=" N   ASN D 396 " --> pdb=" O   PHE D 451 " (cutoff:3.500A)
      removed outlier: 7.901A  pdb=" N   ILE D 453 " --> pdb=" O   ASN D 396 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   VAL D 398 " --> pdb=" O   ILE D 453 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   LEU D 455 " --> pdb=" O   VAL D 398 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   LEU D 400 " --> pdb=" O   LEU D 455 " (cutoff:3.500A)
      removed outlier: 8.520A  pdb=" N   ILE D 487 " --> pdb=" O   ALA D 450 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   ILE D 452 " --> pdb=" O   ILE D 487 " (cutoff:3.500A)
      removed outlier: 7.288A  pdb=" N   PHE D 489 " --> pdb=" O   ILE D 452 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   LEU D 454 " --> pdb=" O   PHE D 489 " (cutoff:3.500A)
      removed outlier: 8.093A  pdb=" N   LEU D 513 " --> pdb=" O   VAL D 486 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 395 through 400
      removed outlier: 6.927A  pdb=" N   ASN A 396 " --> pdb=" O   SER A 449 " (cutoff:3.500A)
      removed outlier: 8.622A  pdb=" N   ILE A 487 " --> pdb=" O   ALA A 450 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   ILE A 452 " --> pdb=" O   ILE A 487 " (cutoff:3.500A)
      removed outlier: 7.335A  pdb=" N   PHE A 489 " --> pdb=" O   ILE A 452 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   LEU A 454 " --> pdb=" O   PHE A 489 " (cutoff:3.500A)
      removed outlier: 8.182A  pdb=" N   LEU A 513 " --> pdb=" O   VAL A 486 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 395 through 400
      removed outlier: 7.008A  pdb=" N   ASN C 396 " --> pdb=" O   PHE C 451 " (cutoff:3.500A)
      removed outlier: 7.705A  pdb=" N   ILE C 453 " --> pdb=" O   ASN C 396 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   VAL C 398 " --> pdb=" O   ILE C 453 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   LEU C 455 " --> pdb=" O   VAL C 398 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   LEU C 400 " --> pdb=" O   LEU C 455 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   ILE C 487 " --> pdb=" O   ALA C 450 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   ILE C 452 " --> pdb=" O   ILE C 487 " (cutoff:3.500A)
      removed outlier: 7.267A  pdb=" N   PHE C 489 " --> pdb=" O   ILE C 452 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   LEU C 454 " --> pdb=" O   PHE C 489 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6

    258 hydrogen bonds defined for protein.
    708 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.46

  Time building geometry restraints manager: 1.91 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: 2290
        1.34 -     1.46: 1183
        1.46 -     1.57: 3289
        1.57 -     1.69: 0
        1.69 -     1.81: 48
  Bond restraints: 6810
  Sorted by residual:
  bond pdb=" C   VAL C 433 "
       pdb=" N   PRO C 434 "
    ideal  model  delta    sigma   weight residual
    1.334  1.358 -0.024 2.34e-02 1.83e+03 1.04e+00
  bond pdb=" C   LEU A 490 "
       pdb=" O   LEU A 490 "
    ideal  model  delta    sigma   weight residual
    1.246  1.237  0.009 9.20e-03 1.18e+04 9.04e-01
  bond pdb=" CD  GLU B 417 "
       pdb=" OE1 GLU B 417 "
    ideal  model  delta    sigma   weight residual
    1.249  1.232  0.017 1.90e-02 2.77e+03 8.13e-01
  bond pdb=" C   SER A 495 "
       pdb=" N   PRO A 496 "
    ideal  model  delta    sigma   weight residual
    1.334  1.341 -0.007 8.40e-03 1.42e+04 7.41e-01
  bond pdb=" C   VAL E 433 "
       pdb=" N   PRO E 434 "
    ideal  model  delta    sigma   weight residual
    1.334  1.353 -0.019 2.34e-02 1.83e+03 6.66e-01
  ... (remaining 6805 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 9096
        1.99 -     3.98: 108
        3.98 -     5.97: 16
        5.97 -     7.95: 0
        7.95 -     9.94: 2
  Bond angle restraints: 9222
  Sorted by residual:
  angle pdb=" N   VAL A 433 "
        pdb=" CA  VAL A 433 "
        pdb=" C   VAL A 433 "
      ideal   model   delta    sigma   weight residual
     112.35  108.85    3.50 1.20e+00 6.94e-01 8.51e+00
  angle pdb=" CA  LEU B 513 "
        pdb=" CB  LEU B 513 "
        pdb=" CG  LEU B 513 "
      ideal   model   delta    sigma   weight residual
     116.30  126.24   -9.94 3.50e+00 8.16e-02 8.07e+00
  angle pdb=" C   PHE A 489 "
        pdb=" N   LEU A 490 "
        pdb=" CA  LEU A 490 "
      ideal   model   delta    sigma   weight residual
     122.42  118.39    4.03 1.52e+00 4.33e-01 7.03e+00
  angle pdb=" C   LEU B 416 "
        pdb=" N   GLU B 417 "
        pdb=" CA  GLU B 417 "
      ideal   model   delta    sigma   weight residual
     120.72  116.44    4.28 1.67e+00 3.59e-01 6.56e+00
  angle pdb=" N   VAL E 433 "
        pdb=" CA  VAL E 433 "
        pdb=" C   VAL E 433 "
      ideal   model   delta    sigma   weight residual
     108.88  114.39   -5.51 2.16e+00 2.14e-01 6.51e+00
  ... (remaining 9217 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 3713
       17.66 -    35.31: 369
       35.31 -    52.96: 52
       52.96 -    70.62: 8
       70.62 -    88.27: 10
  Dihedral angle restraints: 4152
    sinusoidal: 1650
      harmonic: 2502
  Sorted by residual:
  dihedral pdb=" CA  ARG B 512 "
           pdb=" C   ARG B 512 "
           pdb=" N   LEU B 513 "
           pdb=" CA  LEU B 513 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.83   18.17     0      5.00e+00 4.00e-02 1.32e+01
  dihedral pdb=" CA  ARG F 436 "
           pdb=" C   ARG F 436 "
           pdb=" N   GLY F 437 "
           pdb=" CA  GLY F 437 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.27   17.73     0      5.00e+00 4.00e-02 1.26e+01
  dihedral pdb=" CA  PRO D 434 "
           pdb=" C   PRO D 434 "
           pdb=" N   GLY D 435 "
           pdb=" CA  GLY D 435 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.72   17.28     0      5.00e+00 4.00e-02 1.19e+01
  ... (remaining 4149 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 671
       0.028 -    0.056: 247
       0.056 -    0.084: 73
       0.084 -    0.113: 44
       0.113 -    0.141: 21
  Chirality restraints: 1056
  Sorted by residual:
  chirality pdb=" CB  ILE D 519 "
            pdb=" CA  ILE D 519 "
            pdb=" CG1 ILE D 519 "
            pdb=" CG2 ILE D 519 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 4.95e-01
  chirality pdb=" CB  ILE E 519 "
            pdb=" CA  ILE E 519 "
            pdb=" CG1 ILE E 519 "
            pdb=" CG2 ILE E 519 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 4.90e-01
  chirality pdb=" CB  ILE F 519 "
            pdb=" CA  ILE F 519 "
            pdb=" CG1 ILE F 519 "
            pdb=" CG2 ILE F 519 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.13 2.00e-01 2.50e+01 4.54e-01
  ... (remaining 1053 not shown)

  Planarity restraints: 1218
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS F 529 "   -0.034 5.00e-02 4.00e+02   5.11e-02 4.18e+00
        pdb=" N   PRO F 530 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO F 530 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO F 530 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS D 529 "   -0.031 5.00e-02 4.00e+02   4.70e-02 3.54e+00
        pdb=" N   PRO D 530 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO D 530 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO D 530 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS E 529 "    0.029 5.00e-02 4.00e+02   4.50e-02 3.24e+00
        pdb=" N   PRO E 530 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO E 530 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO E 530 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1215 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 714
        2.75 -     3.28: 7002
        3.28 -     3.82: 10709
        3.82 -     4.36: 12153
        4.36 -     4.90: 21247
  Nonbonded interactions: 51825
  Sorted by model distance:
  nonbonded pdb=" O   SER F 501 "
            pdb=" OG  SER F 505 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" NZ  LYS D 415 "
            pdb=" OE2 GLU D 515 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" NH2 ARG E 463 "
            pdb=" O   ARG F 479 "
     model   vdw
     2.244 3.120
  nonbonded pdb=" NH2 ARG F 463 "
            pdb=" O   SER C 482 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" O   ARG B 479 "
            pdb=" NH2 ARG A 463 "
     model   vdw
     2.272 3.120
  ... (remaining 51820 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             0.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     18.800
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.030
  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:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
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   0.035   6810  Z= 0.197
  Angle     :  0.559   9.942   9222  Z= 0.295
  Chirality :  0.039   0.141   1056
  Planarity :  0.004   0.051   1218
  Dihedral  : 14.361  88.273   2508
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.30), residues: 846
  helix:  1.58 (0.28), residues: 348
  sheet: -1.21 (0.49), residues: 120
  loop : -1.35 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F 401 
 PHE   0.018   0.002   PHE D 431 
 TYR   0.009   0.002   TYR D 395 
 ARG   0.003   0.000   ARG F 532 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
REVERT: E  406 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8238 (mm-30)
REVERT: E  423 ASP cc_start: 0.8473 (m-30) cc_final: 0.8247 (m-30)
REVERT: E  461 ASP cc_start: 0.8094 (t0) cc_final: 0.7892 (t0)
REVERT: E  526 ASN cc_start: 0.8244 (m110) cc_final: 0.7811 (m-40)
REVERT: F  429 GLU cc_start: 0.7654 (tp30) cc_final: 0.7414 (tp30)
REVERT: D  423 ASP cc_start: 0.8785 (m-30) cc_final: 0.8569 (m-30)
REVERT: A  461 ASP cc_start: 0.8528 (t0) cc_final: 0.8315 (t0)
REVERT: C  406 GLU cc_start: 0.8610 (mp0) cc_final: 0.8102 (mp0)
REVERT: C  431 PHE cc_start: 0.8489 (t80) cc_final: 0.8276 (t80)
REVERT: C  484 ASP cc_start: 0.8233 (t0) cc_final: 0.7936 (t0)
REVERT: C  526 ASN cc_start: 0.8644 (t0) cc_final: 0.8381 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 225
  average time/residue: 0.2639
  time to fit residues: 72.3345
Evaluate side-chains
  191 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    5.9990
   chunk 63 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
E 459 ASN
E 471 GLN
** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 459 ASN
C 470 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.135083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.105404 restraints weight = 9883.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 3.78
r_work: 0.3332 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.1497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6810  Z= 0.287
  Angle     :  0.594   7.266   9222  Z= 0.314
  Chirality :  0.042   0.314   1056
  Planarity :  0.005   0.052   1218
  Dihedral  :  4.680  20.676    912
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  :  9.89 %
    Favored  : 88.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.31), residues: 846
  helix:  1.96 (0.30), residues: 312
  sheet: -1.29 (0.50), residues: 120
  loop : -1.13 (0.33), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 401 
 PHE   0.029   0.002   PHE A 431 
 TYR   0.014   0.002   TYR F 395 
 ARG   0.007   0.001   ARG E 403 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 204
  time to evaluate  : 0.797 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  406 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8321 (mm-30)
REVERT: E  423 ASP cc_start: 0.8650 (m-30) cc_final: 0.8416 (m-30)
REVERT: E  429 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7612 (tm-30)
REVERT: E  526 ASN cc_start: 0.8234 (m110) cc_final: 0.7776 (m-40)
REVERT: B  395 TYR cc_start: 0.8669 (m-80) cc_final: 0.8434 (m-10)
REVERT: B  406 GLU cc_start: 0.8432 (mp0) cc_final: 0.8194 (mp0)
REVERT: B  447 ASP cc_start: 0.8944 (m-30) cc_final: 0.8666 (m-30)
REVERT: F  429 GLU cc_start: 0.8013 (tp30) cc_final: 0.7793 (tp30)
REVERT: F  436 ARG cc_start: 0.7071 (mmt180) cc_final: 0.6775 (mmt180)
REVERT: F  520 PHE cc_start: 0.7631 (t80) cc_final: 0.7292 (t80)
REVERT: D  423 ASP cc_start: 0.8922 (m-30) cc_final: 0.8681 (m-30)
REVERT: D  512 ARG cc_start: 0.8736 (ptp90) cc_final: 0.8528 (ptp-170)
REVERT: C  406 GLU cc_start: 0.8786 (mp0) cc_final: 0.8256 (mp0)
REVERT: C  431 PHE cc_start: 0.8702 (t80) cc_final: 0.8420 (t80)
REVERT: C  484 ASP cc_start: 0.8449 (t0) cc_final: 0.7989 (t0)
  outliers start: 15
  outliers final: 9
  residues processed: 206
  average time/residue: 0.2610
  time to fit residues: 65.6183
Evaluate side-chains
  203 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 194
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  410 LEU
Chi-restraints excluded: chain B residue  469 VAL
Chi-restraints excluded: chain F residue  416 LEU
Chi-restraints excluded: chain F residue  462 CYS
Chi-restraints excluded: chain F residue  510 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain A residue  532 ARG
Chi-restraints excluded: chain C residue  416 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 82 optimal weight:    5.9990
   chunk 58 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 27 optimal weight:    0.6980
   chunk 71 optimal weight:    7.9990
   chunk 78 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
E 476 ASN
B 407 HIS
** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 459 ASN
** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.135319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.106829 restraints weight = 9956.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 3.63
r_work: 0.3424 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.1658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6810  Z= 0.232
  Angle     :  0.553   7.298   9222  Z= 0.291
  Chirality :  0.040   0.159   1056
  Planarity :  0.005   0.051   1218
  Dihedral  :  4.601  19.469    912
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 13.69 %
    Favored  : 84.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.02 (0.31), residues: 846
  helix:  2.08 (0.30), residues: 306
  sheet: -1.40 (0.50), residues: 120
  loop : -1.15 (0.33), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 401 
 PHE   0.028   0.001   PHE A 431 
 TYR   0.007   0.001   TYR F 395 
 ARG   0.009   0.001   ARG B 413 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 200
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  406 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8250 (mm-30)
REVERT: E  423 ASP cc_start: 0.8641 (m-30) cc_final: 0.8410 (m-30)
REVERT: E  429 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7598 (tm-30)
REVERT: E  526 ASN cc_start: 0.8234 (m110) cc_final: 0.7777 (m-40)
REVERT: B  447 ASP cc_start: 0.8954 (m-30) cc_final: 0.8638 (m-30)
REVERT: B  510 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8518 (mp)
REVERT: F  410 LEU cc_start: 0.8760 (mt) cc_final: 0.8522 (pp)
REVERT: F  462 CYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7999 (m)
REVERT: F  520 PHE cc_start: 0.7630 (t80) cc_final: 0.7381 (t80)
REVERT: D  423 ASP cc_start: 0.8885 (m-30) cc_final: 0.8637 (m-30)
REVERT: D  512 ARG cc_start: 0.8681 (ptp90) cc_final: 0.8452 (ptp-170)
REVERT: A  438 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7915 (mm-30)
REVERT: C  406 GLU cc_start: 0.8735 (mp0) cc_final: 0.8202 (mp0)
REVERT: C  431 PHE cc_start: 0.8677 (t80) cc_final: 0.8407 (t80)
REVERT: C  484 ASP cc_start: 0.8386 (t0) cc_final: 0.7941 (t0)
  outliers start: 15
  outliers final: 6
  residues processed: 202
  average time/residue: 0.2587
  time to fit residues: 64.0497
Evaluate side-chains
  201 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 193
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  490 LEU
Chi-restraints excluded: chain B residue  469 VAL
Chi-restraints excluded: chain B residue  510 LEU
Chi-restraints excluded: chain F residue  416 LEU
Chi-restraints excluded: chain F residue  462 CYS
Chi-restraints excluded: chain F residue  510 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  416 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0970
   chunk 13 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 28 optimal weight:    7.9990
   chunk 6 optimal weight:    7.9990
   chunk 68 optimal weight:    3.9990
   chunk 43 optimal weight:    7.9990
   chunk 60 optimal weight:    3.9990
   chunk 3 optimal weight:   10.0000
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 476 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.133486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.104487 restraints weight = 9991.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 3.73
r_work: 0.3347 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6810  Z= 0.234
  Angle     :  0.556   7.206   9222  Z= 0.294
  Chirality :  0.040   0.156   1056
  Planarity :  0.005   0.051   1218
  Dihedral  :  4.557  19.054    912
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.85 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.31), residues: 846
  helix:  1.75 (0.29), residues: 342
  sheet: -1.49 (0.49), residues: 120
  loop : -1.36 (0.34), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 401 
 PHE   0.029   0.001   PHE A 431 
 TYR   0.008   0.001   TYR F 395 
 ARG   0.007   0.001   ARG E 403 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 194
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  406 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8250 (mm-30)
REVERT: E  423 ASP cc_start: 0.8596 (m-30) cc_final: 0.8375 (m-30)
REVERT: E  429 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7612 (tm-30)
REVERT: E  526 ASN cc_start: 0.8231 (m110) cc_final: 0.7770 (m-40)
REVERT: B  406 GLU cc_start: 0.8446 (mp0) cc_final: 0.8178 (mp0)
REVERT: B  447 ASP cc_start: 0.9014 (m-30) cc_final: 0.8681 (m-30)
REVERT: F  410 LEU cc_start: 0.8754 (mt) cc_final: 0.8513 (pp)
REVERT: F  459 ASN cc_start: 0.8630 (t0) cc_final: 0.8414 (t0)
REVERT: F  462 CYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8023 (m)
REVERT: D  423 ASP cc_start: 0.8891 (m-30) cc_final: 0.8645 (m-30)
REVERT: D  512 ARG cc_start: 0.8550 (ptp90) cc_final: 0.8291 (ptp-170)
REVERT: A  438 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8123 (mm-30)
REVERT: A  493 GLU cc_start: 0.8687 (mp0) cc_final: 0.8475 (mp0)
REVERT: C  406 GLU cc_start: 0.8777 (mp0) cc_final: 0.8218 (mp0)
REVERT: C  484 ASP cc_start: 0.8327 (t0) cc_final: 0.7890 (t0)
  outliers start: 16
  outliers final: 10
  residues processed: 199
  average time/residue: 0.2515
  time to fit residues: 61.7871
Evaluate side-chains
  201 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 190
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  410 LEU
Chi-restraints excluded: chain E residue  490 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  469 VAL
Chi-restraints excluded: chain B residue  510 LEU
Chi-restraints excluded: chain F residue  416 LEU
Chi-restraints excluded: chain F residue  436 ARG
Chi-restraints excluded: chain F residue  462 CYS
Chi-restraints excluded: chain F residue  510 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain C residue  416 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:    0.0000
   chunk 80 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   chunk 3 optimal weight:    8.9990
   chunk 83 optimal weight:    0.6980
   chunk 28 optimal weight:    7.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0020
   chunk 40 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.5192

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

Flipped N/Q/H residues before XYZ refinement:
** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 459 ASN
** F 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.136738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.107852 restraints weight = 9763.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 3.70
r_work: 0.3385 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.2042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6810  Z= 0.173
  Angle     :  0.544   6.865   9222  Z= 0.285
  Chirality :  0.038   0.160   1056
  Planarity :  0.004   0.050   1218
  Dihedral  :  4.355  18.462    912
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 17.75 %
    Favored  : 80.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.31), residues: 846
  helix:  1.89 (0.28), residues: 342
  sheet: -1.45 (0.50), residues: 120
  loop : -1.31 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.000   HIS F 401 
 PHE   0.023   0.001   PHE A 431 
 TYR   0.011   0.002   TYR B 395 
 ARG   0.008   0.001   ARG E 403 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 199
  time to evaluate  : 0.826 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  406 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8276 (mm-30)
REVERT: E  413 ARG cc_start: 0.8044 (tmm-80) cc_final: 0.7802 (ptm160)
REVERT: E  423 ASP cc_start: 0.8600 (m-30) cc_final: 0.8378 (m-30)
REVERT: E  429 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7603 (tm-30)
REVERT: E  526 ASN cc_start: 0.8218 (m110) cc_final: 0.7753 (m-40)
REVERT: B  447 ASP cc_start: 0.9057 (m-30) cc_final: 0.8832 (m-30)
REVERT: F  459 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8442 (t0)
REVERT: F  462 CYS cc_start: 0.8336 (t) cc_final: 0.8063 (m)
REVERT: D  462 CYS cc_start: 0.8514 (p) cc_final: 0.8241 (p)
REVERT: D  512 ARG cc_start: 0.8381 (ptp90) cc_final: 0.8124 (ptp-170)
REVERT: C  406 GLU cc_start: 0.8766 (mp0) cc_final: 0.8245 (mp0)
REVERT: C  431 PHE cc_start: 0.8559 (t80) cc_final: 0.8315 (t80)
REVERT: C  484 ASP cc_start: 0.8239 (t0) cc_final: 0.7829 (t0)
  outliers start: 13
  outliers final: 8
  residues processed: 202
  average time/residue: 0.2462
  time to fit residues: 61.8235
Evaluate side-chains
  197 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 188
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  410 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  469 VAL
Chi-restraints excluded: chain F residue  416 LEU
Chi-restraints excluded: chain F residue  436 ARG
Chi-restraints excluded: chain F residue  459 ASN
Chi-restraints excluded: chain F residue  510 LEU
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain C residue  416 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 82 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   chunk 11 optimal weight:   10.0000
   chunk 19 optimal weight:    2.9990
   chunk 58 optimal weight:    6.9990
   chunk 74 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 476 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.131938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.103290 restraints weight = 9917.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 3.68
r_work: 0.3321 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6810  Z= 0.313
  Angle     :  0.609   7.307   9222  Z= 0.325
  Chirality :  0.041   0.174   1056
  Planarity :  0.005   0.050   1218
  Dihedral  :  4.618  19.627    912
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.57 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 19.51 %
    Favored  : 78.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.31), residues: 846
  helix:  1.83 (0.28), residues: 342
  sheet: -1.57 (0.49), residues: 120
  loop : -1.39 (0.34), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 401 
 PHE   0.029   0.002   PHE A 431 
 TYR   0.008   0.002   TYR F 395 
 ARG   0.010   0.001   ARG E 403 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 188
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  406 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8369 (mm-30)
REVERT: E  413 ARG cc_start: 0.8051 (tmm-80) cc_final: 0.7798 (ptm160)
REVERT: E  414 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7806 (mt-10)
REVERT: E  423 ASP cc_start: 0.8604 (m-30) cc_final: 0.8378 (m-30)
REVERT: E  526 ASN cc_start: 0.8213 (m110) cc_final: 0.7719 (m-40)
REVERT: B  406 GLU cc_start: 0.8372 (mp0) cc_final: 0.8114 (mp0)
REVERT: B  414 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8529 (mt-10)
REVERT: B  447 ASP cc_start: 0.9073 (m-30) cc_final: 0.8774 (m-30)
REVERT: F  429 GLU cc_start: 0.7678 (tp30) cc_final: 0.7325 (tp30)
REVERT: F  459 ASN cc_start: 0.8744 (t0) cc_final: 0.8541 (t0)
REVERT: F  462 CYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8212 (m)
REVERT: D  462 CYS cc_start: 0.8593 (p) cc_final: 0.8311 (p)
REVERT: D  512 ARG cc_start: 0.8437 (ptp90) cc_final: 0.8070 (ptp-170)
REVERT: D  522 ARG cc_start: 0.8805 (ttt-90) cc_final: 0.8152 (tpt-90)
REVERT: A  438 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8197 (mm-30)
REVERT: C  403 ARG cc_start: 0.8436 (tpp80) cc_final: 0.8092 (tpp80)
REVERT: C  406 GLU cc_start: 0.8783 (mp0) cc_final: 0.8270 (mp0)
REVERT: C  484 ASP cc_start: 0.8224 (t0) cc_final: 0.7781 (t0)
  outliers start: 16
  outliers final: 11
  residues processed: 193
  average time/residue: 0.2541
  time to fit residues: 60.3020
Evaluate side-chains
  197 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 185
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  416 LEU
Chi-restraints excluded: chain E residue  478 THR
Chi-restraints excluded: chain E residue  490 LEU
Chi-restraints excluded: chain B residue  417 GLU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  469 VAL
Chi-restraints excluded: chain B residue  510 LEU
Chi-restraints excluded: chain F residue  457 THR
Chi-restraints excluded: chain F residue  462 CYS
Chi-restraints excluded: chain F residue  510 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  416 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 83 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9990
   chunk 38 optimal weight:    8.9990
   chunk 6 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 476 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.135124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.106055 restraints weight = 9882.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 3.73
r_work: 0.3366 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.2277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6810  Z= 0.203
  Angle     :  0.584  14.582   9222  Z= 0.300
  Chirality :  0.039   0.157   1056
  Planarity :  0.005   0.050   1218
  Dihedral  :  4.461  19.075    912
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 20.05 %
    Favored  : 78.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.31), residues: 846
  helix:  1.87 (0.28), residues: 342
  sheet: -1.54 (0.49), residues: 120
  loop : -1.39 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 401 
 PHE   0.026   0.001   PHE A 431 
 TYR   0.010   0.002   TYR B 395 
 ARG   0.007   0.001   ARG A 436 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 197
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  413 ARG cc_start: 0.8014 (tmm-80) cc_final: 0.7781 (ptm160)
REVERT: E  414 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7769 (mt-10)
REVERT: E  429 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7589 (tm-30)
REVERT: E  493 GLU cc_start: 0.8156 (mp0) cc_final: 0.7663 (mp0)
REVERT: E  526 ASN cc_start: 0.8213 (m110) cc_final: 0.7753 (m-40)
REVERT: B  406 GLU cc_start: 0.8375 (mp0) cc_final: 0.8107 (mp0)
REVERT: B  414 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8526 (mt-10)
REVERT: B  447 ASP cc_start: 0.9094 (m-30) cc_final: 0.8821 (m-30)
REVERT: F  462 CYS cc_start: 0.8514 (t) cc_final: 0.8239 (m)
REVERT: D  462 CYS cc_start: 0.8552 (p) cc_final: 0.8247 (p)
REVERT: D  512 ARG cc_start: 0.8328 (ptp90) cc_final: 0.8027 (ptp-170)
REVERT: A  417 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8159 (pt0)
REVERT: C  403 ARG cc_start: 0.8392 (tpp80) cc_final: 0.8061 (tpp80)
REVERT: C  406 GLU cc_start: 0.8800 (mp0) cc_final: 0.8294 (mp0)
REVERT: C  484 ASP cc_start: 0.8155 (t0) cc_final: 0.7756 (t0)
  outliers start: 11
  outliers final: 8
  residues processed: 202
  average time/residue: 0.2564
  time to fit residues: 63.4357
Evaluate side-chains
  197 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 189
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  416 LEU
Chi-restraints excluded: chain B residue  417 GLU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  469 VAL
Chi-restraints excluded: chain B residue  510 LEU
Chi-restraints excluded: chain F residue  436 ARG
Chi-restraints excluded: chain F residue  510 LEU
Chi-restraints excluded: chain A residue  416 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    5.9990
   chunk 54 optimal weight:    0.1980
   chunk 23 optimal weight:    0.7980
   chunk 81 optimal weight:    0.3980
   chunk 83 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 24 optimal weight:    9.9990
   chunk 63 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   chunk 66 optimal weight:    8.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.136517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.107319 restraints weight = 9866.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 3.74
r_work: 0.3375 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6810  Z= 0.189
  Angle     :  0.585  11.781   9222  Z= 0.304
  Chirality :  0.039   0.169   1056
  Planarity :  0.005   0.055   1218
  Dihedral  :  4.350  18.379    912
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 20.60 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.30), residues: 846
  helix:  1.91 (0.28), residues: 342
  sheet: -1.52 (0.49), residues: 120
  loop : -1.45 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 401 
 PHE   0.026   0.001   PHE A 431 
 TYR   0.009   0.002   TYR B 395 
 ARG   0.013   0.001   ARG E 403 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 194
  time to evaluate  : 0.790 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  413 ARG cc_start: 0.8004 (tmm-80) cc_final: 0.7783 (ptm160)
REVERT: E  414 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7893 (mt-10)
REVERT: E  429 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7595 (tm-30)
REVERT: E  493 GLU cc_start: 0.8167 (mp0) cc_final: 0.7673 (mp0)
REVERT: E  526 ASN cc_start: 0.8204 (m110) cc_final: 0.7751 (m-40)
REVERT: B  406 GLU cc_start: 0.8374 (mp0) cc_final: 0.8099 (mp0)
REVERT: B  414 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8541 (mt-10)
REVERT: B  447 ASP cc_start: 0.9094 (m-30) cc_final: 0.8821 (m-30)
REVERT: B  493 GLU cc_start: 0.8787 (mp0) cc_final: 0.8508 (mp0)
REVERT: F  429 GLU cc_start: 0.7598 (tp30) cc_final: 0.7140 (tp30)
REVERT: F  462 CYS cc_start: 0.8462 (t) cc_final: 0.8165 (m)
REVERT: D  462 CYS cc_start: 0.8544 (p) cc_final: 0.8267 (p)
REVERT: D  512 ARG cc_start: 0.8232 (ptp90) cc_final: 0.7949 (ptp-170)
REVERT: D  522 ARG cc_start: 0.8716 (ttt-90) cc_final: 0.8249 (tpt-90)
REVERT: A  417 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8209 (pt0)
REVERT: C  406 GLU cc_start: 0.8908 (mp0) cc_final: 0.8429 (mp0)
  outliers start: 11
  outliers final: 7
  residues processed: 199
  average time/residue: 0.2414
  time to fit residues: 59.7773
Evaluate side-chains
  201 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 194
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  416 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  469 VAL
Chi-restraints excluded: chain B residue  510 LEU
Chi-restraints excluded: chain F residue  436 ARG
Chi-restraints excluded: chain F residue  510 LEU
Chi-restraints excluded: chain A residue  416 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   chunk 59 optimal weight:    5.9990
   chunk 65 optimal weight:    0.6980
   chunk 22 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 57 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 70 optimal weight:    5.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 476 ASN
D 526 ASN
C 443 GLN
C 471 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.135424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.106174 restraints weight = 9996.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 3.77
r_work: 0.3374 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6810  Z= 0.223
  Angle     :  0.611  11.559   9222  Z= 0.319
  Chirality :  0.039   0.180   1056
  Planarity :  0.005   0.058   1218
  Dihedral  :  4.419  18.525    912
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 20.73 %
    Favored  : 77.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.30), residues: 846
  helix:  1.95 (0.28), residues: 342
  sheet: -1.55 (0.49), residues: 120
  loop : -1.47 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 401 
 PHE   0.028   0.001   PHE A 431 
 TYR   0.008   0.001   TYR B 395 
 ARG   0.014   0.001   ARG E 403 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 190
  time to evaluate  : 0.731 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  413 ARG cc_start: 0.8013 (tmm-80) cc_final: 0.7787 (ptm160)
REVERT: E  414 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7860 (mt-10)
REVERT: E  423 ASP cc_start: 0.8591 (m-30) cc_final: 0.8360 (m-30)
REVERT: E  429 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7598 (tm-30)
REVERT: E  493 GLU cc_start: 0.8191 (mp0) cc_final: 0.7684 (mp0)
REVERT: E  526 ASN cc_start: 0.8220 (m110) cc_final: 0.7764 (m-40)
REVERT: B  406 GLU cc_start: 0.8375 (mp0) cc_final: 0.8079 (mp0)
REVERT: B  414 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8512 (mt-10)
REVERT: B  447 ASP cc_start: 0.9104 (m-30) cc_final: 0.8826 (m-30)
REVERT: D  462 CYS cc_start: 0.8561 (p) cc_final: 0.8275 (p)
REVERT: D  522 ARG cc_start: 0.8792 (ttt-90) cc_final: 0.8172 (tpt-90)
REVERT: A  417 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8231 (pt0)
REVERT: C  406 GLU cc_start: 0.8881 (mp0) cc_final: 0.8425 (mp0)
  outliers start: 13
  outliers final: 10
  residues processed: 197
  average time/residue: 0.2409
  time to fit residues: 58.8360
Evaluate side-chains
  197 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 187
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  416 LEU
Chi-restraints excluded: chain E residue  490 LEU
Chi-restraints excluded: chain E residue  510 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  469 VAL
Chi-restraints excluded: chain B residue  510 LEU
Chi-restraints excluded: chain F residue  436 ARG
Chi-restraints excluded: chain F residue  510 LEU
Chi-restraints excluded: chain D residue  526 ASN
Chi-restraints excluded: chain A residue  416 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 81 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 34 optimal weight:    0.3980
   chunk 66 optimal weight:    0.7980
   chunk 42 optimal weight:    5.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
E 468 GLN
** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 526 ASN
** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 476 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.136140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.106772 restraints weight = 9939.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 3.77
r_work: 0.3365 rms_B_bonded: 4.59 restraints_weight: 0.5000
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.2513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6810  Z= 0.215
  Angle     :  0.616  11.309   9222  Z= 0.320
  Chirality :  0.039   0.182   1056
  Planarity :  0.005   0.056   1218
  Dihedral  :  4.406  18.261    912
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 21.27 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.30), residues: 846
  helix:  1.97 (0.28), residues: 342
  sheet: -1.56 (0.49), residues: 120
  loop : -1.50 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 401 
 PHE   0.027   0.001   PHE A 431 
 TYR   0.007   0.001   TYR B 395 
 ARG   0.013   0.001   ARG E 403 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 184
  time to evaluate  : 1.061 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  413 ARG cc_start: 0.8014 (tmm-80) cc_final: 0.7779 (ptm160)
REVERT: E  414 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7880 (mt-10)
REVERT: E  429 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7617 (tm-30)
REVERT: E  493 GLU cc_start: 0.8171 (mp0) cc_final: 0.7666 (mp0)
REVERT: E  526 ASN cc_start: 0.8211 (m110) cc_final: 0.7759 (m-40)
REVERT: B  406 GLU cc_start: 0.8349 (mp0) cc_final: 0.8052 (mp0)
REVERT: B  447 ASP cc_start: 0.9106 (m-30) cc_final: 0.8821 (m-30)
REVERT: F  462 CYS cc_start: 0.8481 (t) cc_final: 0.8155 (t)
REVERT: D  462 CYS cc_start: 0.8559 (p) cc_final: 0.8293 (p)
REVERT: A  417 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8215 (pt0)
REVERT: C  406 GLU cc_start: 0.8852 (mp0) cc_final: 0.8423 (mp0)
  outliers start: 12
  outliers final: 10
  residues processed: 190
  average time/residue: 0.2494
  time to fit residues: 58.9814
Evaluate side-chains
  192 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 182
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  416 LEU
Chi-restraints excluded: chain E residue  490 LEU
Chi-restraints excluded: chain E residue  510 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  469 VAL
Chi-restraints excluded: chain B residue  510 LEU
Chi-restraints excluded: chain F residue  436 ARG
Chi-restraints excluded: chain F residue  510 LEU
Chi-restraints excluded: chain D residue  526 ASN
Chi-restraints excluded: chain A residue  416 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 72 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   chunk 67 optimal weight:    5.9990
   chunk 28 optimal weight:    7.9990
   chunk 30 optimal weight:    5.9990
   chunk 54 optimal weight:    0.0270
   chunk 74 optimal weight:    0.1980
   chunk 57 optimal weight:    8.9990
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 526 ASN
C 476 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.137767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.108458 restraints weight = 9897.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 3.75
r_work: 0.3386 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.2542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6810  Z= 0.193
  Angle     :  0.613  11.262   9222  Z= 0.320
  Chirality :  0.039   0.186   1056
  Planarity :  0.005   0.063   1218
  Dihedral  :  4.342  18.360    912
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 21.68 %
    Favored  : 76.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.30), residues: 846
  helix:  1.98 (0.28), residues: 342
  sheet: -1.54 (0.49), residues: 120
  loop : -1.49 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 401 
 PHE   0.026   0.001   PHE A 431 
 TYR   0.006   0.001   TYR B 395 
 ARG   0.014   0.001   ARG E 403 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3325.21 seconds
wall clock time: 57 minutes 57.50 seconds (3477.50 seconds total)