Starting phenix.real_space_refine
on Tue Feb 11 20:50:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dk8_46946/02_2025/9dk8_46946.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dk8_46946/02_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_46946/02_2025/9dk8_46946.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dk8_46946/02_2025/9dk8_46946.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dk8_46946/02_2025/9dk8_46946.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dk8_46946/02_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-5592/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: 4.07, per 1000 atoms: 0.61
  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: 1.51
  Conformation dependent library (CDL) restraints added in 994.3 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: 1.67

  Time building geometry restraints manager: 1.81 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:             0.910
  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:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     18.030
  Find NCS groups from input model:        0.310
  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:             0.010
  Load rotamer database and sin/cos tables:3.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.990
-------------------------------------------------------------------------------
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  : 0.814 
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: 0.2719
  time to fit residues: 73.8982
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  : 0.786 
-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.133647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.104506 restraints weight = 9876.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 3.70
r_work: 0.3333 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.1508

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= 0.288
  Angle     :  0.595   7.250   9222  Z= 0.315
  Chirality :  0.042   0.334   1056
  Planarity :  0.005   0.052   1218
  Dihedral  :  4.686  20.722    912
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  :  9.76 %
    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:  1.97 (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   0.030   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: 16
    poor density    : 203
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  406 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8317 (mm-30)
REVERT: E  423 ASP cc_start: 0.8656 (m-30) cc_final: 0.8420 (m-30)
REVERT: E  429 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7583 (tm-30)
REVERT: E  526 ASN cc_start: 0.8224 (m110) cc_final: 0.7766 (m-40)
REVERT: B  395 TYR cc_start: 0.8668 (m-80) cc_final: 0.8432 (m-10)
REVERT: B  406 GLU cc_start: 0.8441 (mp0) cc_final: 0.8202 (mp0)
REVERT: B  417 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7800 (pt0)
REVERT: B  447 ASP cc_start: 0.8940 (m-30) cc_final: 0.8677 (m-30)
REVERT: F  429 GLU cc_start: 0.8008 (tp30) cc_final: 0.7785 (tp30)
REVERT: F  436 ARG cc_start: 0.7065 (mmt180) cc_final: 0.6790 (mmt180)
REVERT: F  520 PHE cc_start: 0.7629 (t80) cc_final: 0.7297 (t80)
REVERT: D  423 ASP cc_start: 0.8911 (m-30) cc_final: 0.8669 (m-30)
REVERT: D  512 ARG cc_start: 0.8733 (ptp90) cc_final: 0.8527 (ptp-170)
REVERT: C  406 GLU cc_start: 0.8779 (mp0) cc_final: 0.8230 (mp0)
REVERT: C  431 PHE cc_start: 0.8706 (t80) cc_final: 0.8416 (t80)
REVERT: C  484 ASP cc_start: 0.8451 (t0) cc_final: 0.7986 (t0)
  outliers start: 16
  outliers final: 7
  residues processed: 205
  average time/residue: 0.2793
  time to fit residues: 69.3543
Evaluate side-chains
  202 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 194
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  417 GLU
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 82 optimal weight:    9.9990
   chunk 58 optimal weight:    6.9990
   chunk 55 optimal weight:    0.7980
   chunk 40 optimal weight:    5.9990
   chunk 27 optimal weight:    0.5980
   chunk 71 optimal weight:    7.9990
   chunk 78 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
E 471 GLN
E 476 ASN
B 407 HIS
** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 459 ASN
** F 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.136798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.107068 restraints weight = 9877.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 3.78
r_work: 0.3358 rms_B_bonded: 4.59 restraints_weight: 0.5000
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.1645

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= 0.204
  Angle     :  0.541   7.173   9222  Z= 0.284
  Chirality :  0.039   0.159   1056
  Planarity :  0.005   0.051   1218
  Dihedral  :  4.500  18.476    912
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 14.09 %
    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: -0.07 (0.31), residues: 846
  helix:  1.78 (0.29), residues: 342
  sheet: -1.37 (0.50), residues: 120
  loop : -1.30 (0.33), 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 F 395 
 ARG   0.006   0.001   ARG E 403 

*********************** 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
  212 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 200
  time to evaluate  : 0.744 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  406 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8267 (mm-30)
REVERT: E  423 ASP cc_start: 0.8638 (m-30) cc_final: 0.8408 (m-30)
REVERT: E  429 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7667 (tm-30)
REVERT: E  526 ASN cc_start: 0.8232 (m110) cc_final: 0.7775 (m-40)
REVERT: B  395 TYR cc_start: 0.8683 (m-80) cc_final: 0.8477 (m-10)
REVERT: B  447 ASP cc_start: 0.8979 (m-30) cc_final: 0.8678 (m-30)
REVERT: B  510 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8470 (mp)
REVERT: F  410 LEU cc_start: 0.8749 (mt) cc_final: 0.8509 (pp)
REVERT: F  462 CYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7987 (m)
REVERT: F  520 PHE cc_start: 0.7609 (t80) cc_final: 0.7358 (t80)
REVERT: D  423 ASP cc_start: 0.8919 (m-30) cc_final: 0.8671 (m-30)
REVERT: D  512 ARG cc_start: 0.8653 (ptp90) cc_final: 0.8438 (ptp-170)
REVERT: D  526 ASN cc_start: 0.8791 (t0) cc_final: 0.8572 (m-40)
REVERT: A  438 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7937 (mm-30)
REVERT: C  406 GLU cc_start: 0.8784 (mp0) cc_final: 0.8228 (mp0)
REVERT: C  431 PHE cc_start: 0.8607 (t80) cc_final: 0.8345 (t80)
REVERT: C  484 ASP cc_start: 0.8377 (t0) cc_final: 0.7915 (t0)
  outliers start: 12
  outliers final: 5
  residues processed: 202
  average time/residue: 0.2636
  time to fit residues: 65.2623
Evaluate side-chains
  200 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 193
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  410 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 C 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:    0.8980
   chunk 59 optimal weight:    0.7980
   chunk 13 optimal weight:    7.9990
   chunk 62 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 28 optimal weight:    7.9990
   chunk 6 optimal weight:    0.7980
   chunk 68 optimal weight:    4.9990
   chunk 43 optimal weight:    8.9990
   chunk 60 optimal weight:    0.0020
   chunk 3 optimal weight:    9.9990
   overall best weight:    0.6188

-------------------------------------------------------------------------------
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 = 0.3941 r_free = 0.3941 target = 0.136822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.107568 restraints weight = 9890.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 3.75
r_work: 0.3375 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.1862

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= 0.177
  Angle     :  0.531   6.884   9222  Z= 0.279
  Chirality :  0.039   0.155   1056
  Planarity :  0.004   0.050   1218
  Dihedral  :  4.340  18.380    912
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 16.26 %
    Favored  : 81.57 %
  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: -0.01 (0.31), residues: 846
  helix:  1.88 (0.28), residues: 342
  sheet: -1.35 (0.50), residues: 120
  loop : -1.33 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F 401 
 PHE   0.026   0.001   PHE A 431 
 TYR   0.009   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
  219 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 203
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  406 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8268 (mm-30)
REVERT: E  423 ASP cc_start: 0.8656 (m-30) cc_final: 0.8415 (m-30)
REVERT: E  429 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7655 (tm-30)
REVERT: E  526 ASN cc_start: 0.8219 (m110) cc_final: 0.7764 (m-40)
REVERT: B  406 GLU cc_start: 0.8455 (mp0) cc_final: 0.8180 (mp0)
REVERT: B  447 ASP cc_start: 0.9036 (m-30) cc_final: 0.8820 (m-30)
REVERT: F  429 GLU cc_start: 0.7519 (tp30) cc_final: 0.7310 (tp30)
REVERT: F  459 ASN cc_start: 0.8642 (t0) cc_final: 0.8436 (t0)
REVERT: F  462 CYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7978 (m)
REVERT: F  520 PHE cc_start: 0.7685 (t80) cc_final: 0.7442 (t80)
REVERT: D  423 ASP cc_start: 0.8917 (m-30) cc_final: 0.8671 (m-30)
REVERT: D  512 ARG cc_start: 0.8391 (ptp90) cc_final: 0.8149 (ptp-170)
REVERT: A  417 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8219 (pt0)
REVERT: A  438 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7815 (mm-30)
REVERT: C  406 GLU cc_start: 0.8797 (mp0) cc_final: 0.8267 (mp0)
REVERT: C  431 PHE cc_start: 0.8529 (t80) cc_final: 0.8263 (t80)
REVERT: C  484 ASP cc_start: 0.8275 (t0) cc_final: 0.7836 (t0)
  outliers start: 16
  outliers final: 10
  residues processed: 207
  average time/residue: 0.2752
  time to fit residues: 70.1068
Evaluate side-chains
  204 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 193
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
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 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 A residue  416 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:    0.8980
   chunk 80 optimal weight:    0.4980
   chunk 32 optimal weight:    4.9990
   chunk 3 optimal weight:    9.9990
   chunk 83 optimal weight:    5.9990
   chunk 28 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 24 optimal weight:    0.0010
   chunk 40 optimal weight:    0.8980
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.6386

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.137434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.108479 restraints weight = 9762.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3569 rms_B_bonded: 3.73
r_work: 0.3395 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.2023

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= 0.178
  Angle     :  0.542   6.712   9222  Z= 0.286
  Chirality :  0.039   0.158   1056
  Planarity :  0.004   0.050   1218
  Dihedral  :  4.233  18.432    912
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 18.29 %
    Favored  : 79.67 %
  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:  0.04 (0.31), residues: 846
  helix:  1.95 (0.28), residues: 342
  sheet: -1.35 (0.50), residues: 120
  loop : -1.32 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 401 
 PHE   0.025   0.001   PHE A 431 
 TYR   0.011   0.001   TYR F 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: 15
    poor density    : 197
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  406 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8301 (mm-30)
REVERT: E  413 ARG cc_start: 0.8069 (tmm-80) cc_final: 0.7811 (ptm160)
REVERT: E  429 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7637 (tm-30)
REVERT: E  526 ASN cc_start: 0.8215 (m110) cc_final: 0.7759 (m-40)
REVERT: B  447 ASP cc_start: 0.9055 (m-30) cc_final: 0.8825 (m-30)
REVERT: F  459 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8427 (t0)
REVERT: F  462 CYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7934 (m)
REVERT: D  423 ASP cc_start: 0.8908 (m-30) cc_final: 0.8660 (m-30)
REVERT: D  462 CYS cc_start: 0.8556 (p) cc_final: 0.8268 (p)
REVERT: D  512 ARG cc_start: 0.8310 (ptp90) cc_final: 0.8052 (ptp-170)
REVERT: A  417 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8227 (pt0)
REVERT: C  406 GLU cc_start: 0.8802 (mp0) cc_final: 0.8282 (mp0)
REVERT: C  431 PHE cc_start: 0.8548 (t80) cc_final: 0.8284 (t80)
REVERT: C  484 ASP cc_start: 0.8250 (t0) cc_final: 0.7815 (t0)
  outliers start: 15
  outliers final: 9
  residues processed: 200
  average time/residue: 0.2516
  time to fit residues: 61.8587
Evaluate side-chains
  203 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 192
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
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 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  459 ASN
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 82 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9990
   chunk 11 optimal weight:   10.0000
   chunk 19 optimal weight:    4.9990
   chunk 58 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0000
   chunk 26 optimal weight:    0.6980
   chunk 9 optimal weight:    3.9990
   overall best weight:    1.9390

-------------------------------------------------------------------------------
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
A 476 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.132858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.104121 restraints weight = 9864.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 3.69
r_work: 0.3343 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.2159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6810  Z= 0.287
  Angle     :  0.582   7.106   9222  Z= 0.309
  Chirality :  0.041   0.173   1056
  Planarity :  0.005   0.050   1218
  Dihedral  :  4.475  18.680    912
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 19.78 %
    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: -0.02 (0.31), residues: 846
  helix:  1.94 (0.28), residues: 342
  sheet: -1.47 (0.49), residues: 120
  loop : -1.36 (0.33), 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   0.010   0.002   TYR B 395 
 ARG   0.009   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
  202 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 188
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  413 ARG cc_start: 0.8067 (tmm-80) cc_final: 0.7801 (ptm160)
REVERT: E  414 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7864 (mt-10)
REVERT: E  423 ASP cc_start: 0.8604 (m-30) cc_final: 0.8373 (m-30)
REVERT: E  493 GLU cc_start: 0.8188 (mp0) cc_final: 0.7722 (mp0)
REVERT: E  526 ASN cc_start: 0.8212 (m110) cc_final: 0.7730 (m-40)
REVERT: B  406 GLU cc_start: 0.8369 (mp0) cc_final: 0.8118 (mp0)
REVERT: B  447 ASP cc_start: 0.9048 (m-30) cc_final: 0.8743 (m-30)
REVERT: F  462 CYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8254 (m)
REVERT: D  512 ARG cc_start: 0.8404 (ptp90) cc_final: 0.8168 (ptp-170)
REVERT: A  438 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7950 (mm-30)
REVERT: C  406 GLU cc_start: 0.8783 (mp0) cc_final: 0.8261 (mp0)
REVERT: C  484 ASP cc_start: 0.8233 (t0) cc_final: 0.7778 (t0)
  outliers start: 14
  outliers final: 8
  residues processed: 192
  average time/residue: 0.2373
  time to fit residues: 56.4534
Evaluate side-chains
  192 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 183
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 38 optimal weight:    9.9990
   chunk 6 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 62 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   overall best weight:    1.4984

-------------------------------------------------------------------------------
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 = 0.3897 r_free = 0.3897 target = 0.133314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.104510 restraints weight = 9896.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 3.70
r_work: 0.3343 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6810  Z= 0.245
  Angle     :  0.596  15.294   9222  Z= 0.308
  Chirality :  0.040   0.162   1056
  Planarity :  0.005   0.050   1218
  Dihedral  :  4.483  19.446    912
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 20.19 %
    Favored  : 78.18 %
  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: -0.06 (0.30), residues: 846
  helix:  1.93 (0.28), residues: 342
  sheet: -1.53 (0.49), residues: 120
  loop : -1.40 (0.33), 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   0.009   0.001   TYR F 395 
 ARG   0.010   0.001   ARG E 403 

*********************** 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
  203 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 191
  time to evaluate  : 0.748 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  413 ARG cc_start: 0.8068 (tmm-80) cc_final: 0.7809 (ptm160)
REVERT: E  414 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7806 (mt-10)
REVERT: E  429 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7576 (tm-30)
REVERT: E  493 GLU cc_start: 0.8169 (mp0) cc_final: 0.7677 (mp0)
REVERT: E  526 ASN cc_start: 0.8227 (m110) cc_final: 0.7745 (m-40)
REVERT: B  406 GLU cc_start: 0.8385 (mp0) cc_final: 0.8121 (mp0)
REVERT: B  414 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8556 (mt-10)
REVERT: B  447 ASP cc_start: 0.9077 (m-30) cc_final: 0.8799 (m-30)
REVERT: F  462 CYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8229 (m)
REVERT: D  462 CYS cc_start: 0.8564 (p) cc_final: 0.8329 (p)
REVERT: D  512 ARG cc_start: 0.8372 (ptp90) cc_final: 0.8106 (ptp-170)
REVERT: A  438 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8124 (mm-30)
REVERT: C  403 ARG cc_start: 0.8409 (tpp80) cc_final: 0.8097 (tpp80)
REVERT: C  406 GLU cc_start: 0.8772 (mp0) cc_final: 0.8249 (mp0)
  outliers start: 12
  outliers final: 9
  residues processed: 196
  average time/residue: 0.2533
  time to fit residues: 61.1206
Evaluate side-chains
  194 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 184
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
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  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 C 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:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 81 optimal weight:    6.9990
   chunk 83 optimal weight:    0.6980
   chunk 14 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 78 optimal weight:    1.9990
   chunk 66 optimal weight:    7.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 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 = 0.3921 r_free = 0.3921 target = 0.135183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.106225 restraints weight = 9906.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 3.73
r_work: 0.3369 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.2406

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= 0.211
  Angle     :  0.601  12.144   9222  Z= 0.314
  Chirality :  0.039   0.172   1056
  Planarity :  0.005   0.055   1218
  Dihedral  :  4.451  19.210    912
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  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: -0.06 (0.30), residues: 846
  helix:  1.98 (0.28), residues: 342
  sheet: -1.56 (0.49), residues: 120
  loop : -1.43 (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   0.001   TYR F 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
  202 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 189
  time to evaluate  : 0.798 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  413 ARG cc_start: 0.8050 (tmm-80) cc_final: 0.7764 (ptm160)
REVERT: E  414 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7895 (mt-10)
REVERT: E  429 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7607 (tm-30)
REVERT: E  493 GLU cc_start: 0.8184 (mp0) cc_final: 0.7695 (mp0)
REVERT: E  526 ASN cc_start: 0.8223 (m110) cc_final: 0.7768 (m-40)
REVERT: B  406 GLU cc_start: 0.8360 (mp0) cc_final: 0.8094 (mp0)
REVERT: B  414 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8464 (mt-10)
REVERT: B  447 ASP cc_start: 0.9099 (m-30) cc_final: 0.8832 (m-30)
REVERT: F  462 CYS cc_start: 0.8505 (t) cc_final: 0.8178 (m)
REVERT: D  462 CYS cc_start: 0.8570 (p) cc_final: 0.8305 (p)
REVERT: D  512 ARG cc_start: 0.8306 (ptp90) cc_final: 0.8030 (ptp-170)
REVERT: C  406 GLU cc_start: 0.8856 (mp0) cc_final: 0.8370 (mp0)
  outliers start: 13
  outliers final: 9
  residues processed: 195
  average time/residue: 0.2494
  time to fit residues: 60.1961
Evaluate side-chains
  193 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 184
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  416 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 A residue  416 LEU
Chi-restraints excluded: chain C 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:    5.9990
   chunk 45 optimal weight:    0.3980
   chunk 59 optimal weight:    5.9990
   chunk 65 optimal weight:    0.5980
   chunk 22 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 70 optimal weight:    5.9990
   overall best weight:    0.6580

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.136993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.107767 restraints weight = 9908.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 3.77
r_work: 0.3382 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.2438

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= 0.194
  Angle     :  0.599  11.630   9222  Z= 0.313
  Chirality :  0.039   0.186   1056
  Planarity :  0.005   0.050   1218
  Dihedral  :  4.331  18.366    912
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  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: -0.03 (0.30), residues: 846
  helix:  2.02 (0.28), residues: 342
  sheet: -1.50 (0.49), residues: 120
  loop : -1.47 (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   0.011   0.001   TYR F 395 
 ARG   0.013   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
  205 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 193
  time to evaluate  : 0.886 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  413 ARG cc_start: 0.8032 (tmm-80) cc_final: 0.7755 (ptm160)
REVERT: E  414 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7894 (mt-10)
REVERT: E  429 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7613 (tm-30)
REVERT: E  493 GLU cc_start: 0.8167 (mp0) cc_final: 0.7677 (mp0)
REVERT: E  526 ASN cc_start: 0.8207 (m110) cc_final: 0.7758 (m-40)
REVERT: B  406 GLU cc_start: 0.8335 (mp0) cc_final: 0.8066 (mp0)
REVERT: B  414 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8471 (mt-10)
REVERT: B  447 ASP cc_start: 0.9091 (m-30) cc_final: 0.8807 (m-30)
REVERT: F  462 CYS cc_start: 0.8459 (t) cc_final: 0.8141 (m)
REVERT: D  462 CYS cc_start: 0.8560 (p) cc_final: 0.8296 (p)
REVERT: D  512 ARG cc_start: 0.8193 (ptp90) cc_final: 0.7938 (ptp-170)
REVERT: A  417 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8237 (pt0)
REVERT: C  406 GLU cc_start: 0.8874 (mp0) cc_final: 0.8393 (mp0)
REVERT: C  479 ARG cc_start: 0.7425 (ttp-170) cc_final: 0.7139 (tmm-80)
  outliers start: 12
  outliers final: 7
  residues processed: 198
  average time/residue: 0.2678
  time to fit residues: 65.8530
Evaluate side-chains
  195 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 188
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  416 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  410 LEU
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:    0.1980
   chunk 81 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 30 optimal weight:    6.9990
   chunk 63 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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**
F 476 ASN
D 526 ASN
C 476 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.137477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.108177 restraints weight = 9906.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 3.78
r_work: 0.3385 rms_B_bonded: 4.64 restraints_weight: 0.5000
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.2560

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= 0.208
  Angle     :  0.618  11.342   9222  Z= 0.325
  Chirality :  0.039   0.185   1056
  Planarity :  0.005   0.059   1218
  Dihedral  :  4.357  18.516    912
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 21.41 %
    Favored  : 77.24 %
  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: -0.05 (0.30), residues: 846
  helix:  2.02 (0.28), residues: 342
  sheet: -1.48 (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   0.012   0.001   TYR F 395 
 ARG   0.014   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
  195 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 185
  time to evaluate  : 0.795 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  413 ARG cc_start: 0.8033 (tmm-80) cc_final: 0.7750 (ptm160)
REVERT: E  414 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7891 (mt-10)
REVERT: E  429 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7681 (tm-30)
REVERT: E  493 GLU cc_start: 0.8197 (mp0) cc_final: 0.7698 (mp0)
REVERT: E  526 ASN cc_start: 0.8231 (m110) cc_final: 0.7776 (m-40)
REVERT: B  406 GLU cc_start: 0.8331 (mp0) cc_final: 0.8062 (mp0)
REVERT: B  414 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8449 (mt-10)
REVERT: B  447 ASP cc_start: 0.9104 (m-30) cc_final: 0.8831 (m-30)
REVERT: D  462 CYS cc_start: 0.8552 (p) cc_final: 0.8302 (p)
REVERT: A  417 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8200 (pt0)
REVERT: C  406 GLU cc_start: 0.8850 (mp0) cc_final: 0.8406 (mp0)
  outliers start: 10
  outliers final: 8
  residues processed: 189
  average time/residue: 0.2453
  time to fit residues: 57.6004
Evaluate side-chains
  191 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 183
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  416 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  410 LEU
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:    0.9990
   chunk 50 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 67 optimal weight:    0.3980
   chunk 28 optimal weight:    7.9990
   chunk 30 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0060
   chunk 74 optimal weight:    0.7980
   chunk 57 optimal weight:    8.9990
   overall best weight:    0.8400

-------------------------------------------------------------------------------
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**
** F 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 526 ASN
** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 459 ASN
C 476 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.137371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.108044 restraints weight = 9916.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 3.77
r_work: 0.3384 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.2549

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= 0.211
  Angle     :  0.620  11.131   9222  Z= 0.325
  Chirality :  0.039   0.184   1056
  Planarity :  0.005   0.058   1218
  Dihedral  :  4.325  18.261    912
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 21.68 %
    Favored  : 76.96 %
  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: -0.03 (0.30), residues: 846
  helix:  2.02 (0.28), residues: 342
  sheet: -1.44 (0.49), residues: 120
  loop : -1.47 (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   0.013   0.002   TYR F 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: 3145.75 seconds
wall clock time: 56 minutes 46.83 seconds (3406.83 seconds total)