Starting phenix.real_space_refine
on Mon Jul 28 05:55:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dnz_30791/07_2025/7dnz_30791.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dnz_30791/07_2025/7dnz_30791.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dnz_30791/07_2025/7dnz_30791.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dnz_30791/07_2025/7dnz_30791.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dnz_30791/07_2025/7dnz_30791.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dnz_30791/07_2025/7dnz_30791.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.046
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: 5
    Type Number    sf(0)   Gaussians
     Fe      1      7.16       5
     S      38      5.16       5
     C    6256      2.51       5
     N    1634      2.21       5
     O    1742      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9671
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4669
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 591, 4669
          Classifications: {'peptide': 591}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 13, 'TRANS': 577}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "B"
      Number of atoms: 4669
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 591, 4669
          Classifications: {'peptide': 591}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 13, 'TRANS': 577}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "A"
      Number of atoms: 145
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 145
          Unusual residues: {'GSH': 2, 'Y01': 3}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "B"
      Number of atoms: 188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 188
          Unusual residues: {'GSH': 2, 'HEM': 1, 'Y01': 3}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
  Time building chain proxies: 6.76, per 1000 atoms: 0.70
  Number of scatterers: 9671
  At special positions: 0
  Unit cell: (80.51, 98.77, 137.78, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      1     26.01
     S      38     16.00
     O    1742      8.00
     N    1634      7.00
     C    6256      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.64
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2176

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 8 sheets defined
      70.7% alpha, 5.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 239 through 254
      removed outlier: 3.610A  pdb=" N   GLY A 243 " --> pdb=" O   TRP A 239 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   ARG A 244 " --> pdb=" O   ARG A 240 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   LYS A 245 " --> pdb=" O   ASP A 241 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   TRP A 254 " --> pdb=" O   SER A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 295
      removed outlier: 4.006A  pdb=" N   VAL A 280 " --> pdb=" O   ARG A 276 " (cutoff:3.500A)
      Proline residue:  A 283  - end of helix
      removed outlier: 3.656A  pdb=" N   GLU A 295 " --> pdb=" O   ASN A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 316
      removed outlier: 3.637A  pdb=" N   LEU A 302 " --> pdb=" O   PRO A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 355
      removed outlier: 3.512A  pdb=" N   ARG A 330 " --> pdb=" O   VAL A 326 " (cutoff:3.500A)
      removed outlier: 4.887A  pdb=" N   ARG A 336 " --> pdb=" O   PHE A 332 " (cutoff:3.500A)
      removed outlier: 5.129A  pdb=" N   VAL A 337 " --> pdb=" O   LEU A 333 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLN A 338 " --> pdb=" O   TRP A 334 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLN A 339 " --> pdb=" O   ILE A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 364
      removed outlier: 3.946A  pdb=" N   HIS A 361 " --> pdb=" O   SER A 357 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLY A 363 " --> pdb=" O   ARG A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 390
      removed outlier: 3.806A  pdb=" N   VAL A 369 " --> pdb=" O   ARG A 365 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   LEU A 370 " --> pdb=" O   THR A 366 " (cutoff:3.500A)
      removed outlier: 5.177A  pdb=" N   ARG A 371 " --> pdb=" O   GLY A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 409
    Processing helix  chain 'A' and resid 410 through 459
      removed outlier: 3.700A  pdb=" N   GLY A 414 " --> pdb=" O   ASN A 410 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   LYS A 437 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   PHE A 438 " --> pdb=" O   TRP A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 467
      removed outlier: 3.513A  pdb=" N   ASN A 467 " --> pdb=" O   VAL A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 522
      removed outlier: 4.276A  pdb=" N   LYS A 489 " --> pdb=" O   GLY A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 545
      removed outlier: 4.327A  pdb=" N   VAL A 531 " --> pdb=" O   VAL A 527 " (cutoff:3.500A)
      Proline residue:  A 543  - end of helix
    Processing helix  chain 'A' and resid 546 through 570
      removed outlier: 3.699A  pdb=" N   TYR A 550 " --> pdb=" O   TRP A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 637
    Processing helix  chain 'A' and resid 658 through 665
    Processing helix  chain 'A' and resid 680 through 685
    Processing helix  chain 'A' and resid 692 through 704
    Processing helix  chain 'A' and resid 705 through 712
    Processing helix  chain 'A' and resid 728 through 744
    Processing helix  chain 'A' and resid 758 through 773
    Processing helix  chain 'A' and resid 784 through 790
    Processing helix  chain 'A' and resid 807 through 815
    Processing helix  chain 'A' and resid 816 through 825
      removed outlier: 3.672A  pdb=" N   ASP A 820 " --> pdb=" O   GLY A 816 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 239 through 254
      removed outlier: 3.610A  pdb=" N   GLY B 243 " --> pdb=" O   TRP B 239 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   ARG B 244 " --> pdb=" O   ARG B 240 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   LYS B 245 " --> pdb=" O   ASP B 241 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   TRP B 254 " --> pdb=" O   SER B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 295
      removed outlier: 4.006A  pdb=" N   VAL B 280 " --> pdb=" O   ARG B 276 " (cutoff:3.500A)
      Proline residue:  B 283  - end of helix
      removed outlier: 3.656A  pdb=" N   GLU B 295 " --> pdb=" O   ASN B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 316
      removed outlier: 3.638A  pdb=" N   LEU B 302 " --> pdb=" O   PRO B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 355
      removed outlier: 4.887A  pdb=" N   ARG B 336 " --> pdb=" O   PHE B 332 " (cutoff:3.500A)
      removed outlier: 5.128A  pdb=" N   VAL B 337 " --> pdb=" O   LEU B 333 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLN B 338 " --> pdb=" O   TRP B 334 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLN B 339 " --> pdb=" O   ILE B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 364
      removed outlier: 3.946A  pdb=" N   HIS B 361 " --> pdb=" O   SER B 357 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLY B 363 " --> pdb=" O   ARG B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 390
      removed outlier: 3.805A  pdb=" N   VAL B 369 " --> pdb=" O   ARG B 365 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   LEU B 370 " --> pdb=" O   THR B 366 " (cutoff:3.500A)
      removed outlier: 5.177A  pdb=" N   ARG B 371 " --> pdb=" O   GLY B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 409
    Processing helix  chain 'B' and resid 410 through 459
      removed outlier: 3.700A  pdb=" N   GLY B 414 " --> pdb=" O   ASN B 410 " (cutoff:3.500A)
      removed outlier: 5.297A  pdb=" N   LYS B 437 " --> pdb=" O   GLU B 433 " (cutoff:3.500A)
      removed outlier: 4.914A  pdb=" N   PHE B 438 " --> pdb=" O   TRP B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 467
      removed outlier: 3.513A  pdb=" N   ASN B 467 " --> pdb=" O   VAL B 463 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 468 through 522
      removed outlier: 4.276A  pdb=" N   LYS B 489 " --> pdb=" O   GLY B 485 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 527 through 545
      removed outlier: 4.327A  pdb=" N   VAL B 531 " --> pdb=" O   VAL B 527 " (cutoff:3.500A)
      Proline residue:  B 543  - end of helix
    Processing helix  chain 'B' and resid 546 through 570
      removed outlier: 3.699A  pdb=" N   TYR B 550 " --> pdb=" O   TRP B 546 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 627 through 637
    Processing helix  chain 'B' and resid 658 through 665
    Processing helix  chain 'B' and resid 680 through 685
    Processing helix  chain 'B' and resid 692 through 704
    Processing helix  chain 'B' and resid 705 through 712
    Processing helix  chain 'B' and resid 728 through 744
    Processing helix  chain 'B' and resid 758 through 773
    Processing helix  chain 'B' and resid 784 through 790
    Processing helix  chain 'B' and resid 807 through 815
    Processing helix  chain 'B' and resid 816 through 825
      removed outlier: 3.671A  pdb=" N   ASP B 820 " --> pdb=" O   GLY B 816 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 590 through 596
      removed outlier: 3.524A  pdb=" N   GLU A 591 " --> pdb=" O   ARG A 648 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ARG A 648 " --> pdb=" O   GLU A 591 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLU A 593 " --> pdb=" O   CYS A 646 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   CYS A 646 " --> pdb=" O   GLU A 593 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   VAL A 595 " --> pdb=" O   SER A 644 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   SER A 644 " --> pdb=" O   VAL A 595 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 618 through 621
      removed outlier: 3.652A  pdb=" N   ILE A 779 " --> pdb=" O   ILE A 748 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   VAL A 781 " --> pdb=" O   LEU A 750 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 678 through 679
    Processing sheet with id=AA4, first strand: chain 'A' and resid 794 through 798
      removed outlier: 3.839A  pdb=" N   GLY A 806 " --> pdb=" O   ILE A 794 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLU A 804 " --> pdb=" O   VAL A 796 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   LYS A 798 " --> pdb=" O   ILE A 802 " (cutoff:3.500A)
      removed outlier: 5.790A  pdb=" N   ILE A 802 " --> pdb=" O   LYS A 798 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 590 through 596
      removed outlier: 3.525A  pdb=" N   GLU B 591 " --> pdb=" O   ARG B 648 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ARG B 648 " --> pdb=" O   GLU B 591 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLU B 593 " --> pdb=" O   CYS B 646 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   CYS B 646 " --> pdb=" O   GLU B 593 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   VAL B 595 " --> pdb=" O   SER B 644 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   SER B 644 " --> pdb=" O   VAL B 595 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 618 through 621
      removed outlier: 3.652A  pdb=" N   ILE B 779 " --> pdb=" O   ILE B 748 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   VAL B 781 " --> pdb=" O   LEU B 750 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 678 through 679
    Processing sheet with id=AA8, first strand: chain 'B' and resid 794 through 798
      removed outlier: 3.839A  pdb=" N   GLY B 806 " --> pdb=" O   ILE B 794 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLU B 804 " --> pdb=" O   VAL B 796 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   LYS B 798 " --> pdb=" O   ILE B 802 " (cutoff:3.500A)
      removed outlier: 5.790A  pdb=" N   ILE B 802 " --> pdb=" O   LYS B 798 " (cutoff:3.500A)

    625 hydrogen bonds defined for protein.
    1857 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: 2.68

  Time building geometry restraints manager: 3.04 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.20 -     1.38: 3768
        1.38 -     1.56: 6038
        1.56 -     1.74: 4
        1.74 -     1.92: 61
        1.92 -     2.10: 3
  Bond restraints: 9874
  Sorted by residual:
  bond pdb=" C3C HEM B 901 "
       pdb=" CAC HEM B 901 "
    ideal  model  delta    sigma   weight residual
    1.544  1.471  0.073 2.00e-02 2.50e+03 1.34e+01
  bond pdb=" C3B HEM B 901 "
       pdb=" CAB HEM B 901 "
    ideal  model  delta    sigma   weight residual
    1.544  1.475  0.069 2.00e-02 2.50e+03 1.21e+01
  bond pdb=" C1  GSH B 903 "
       pdb=" O12 GSH B 903 "
    ideal  model  delta    sigma   weight residual
    1.307  1.244  0.063 1.90e-02 2.77e+03 1.09e+01
  bond pdb=" C1  GSH A 902 "
       pdb=" O12 GSH A 902 "
    ideal  model  delta    sigma   weight residual
    1.307  1.245  0.062 1.90e-02 2.77e+03 1.07e+01
  bond pdb=" C1  GSH B 902 "
       pdb=" O11 GSH B 902 "
    ideal  model  delta    sigma   weight residual
    1.213  1.246 -0.033 1.00e-02 1.00e+04 1.06e+01
  ... (remaining 9869 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 12524
        1.99 -     3.97: 724
        3.97 -     5.96: 132
        5.96 -     7.94: 34
        7.94 -     9.93: 18
  Bond angle restraints: 13432
  Sorted by residual:
  angle pdb=" C   PHE B 325 "
        pdb=" N   VAL B 326 "
        pdb=" CA  VAL B 326 "
      ideal   model   delta    sigma   weight residual
     122.63  113.76    8.87 1.19e+00 7.06e-01 5.56e+01
  angle pdb=" C   THR A 320 "
        pdb=" CA  THR A 320 "
        pdb=" CB  THR A 320 "
      ideal   model   delta    sigma   weight residual
     109.72  119.03   -9.31 1.66e+00 3.63e-01 3.15e+01
  angle pdb=" N   GLY A 318 "
        pdb=" CA  GLY A 318 "
        pdb=" C   GLY A 318 "
      ideal   model   delta    sigma   weight residual
     112.73  106.03    6.70 1.20e+00 6.94e-01 3.12e+01
  angle pdb=" N   VAL A 280 "
        pdb=" CA  VAL A 280 "
        pdb=" C   VAL A 280 "
      ideal   model   delta    sigma   weight residual
     112.96  108.41    4.55 1.00e+00 1.00e+00 2.07e+01
  angle pdb=" N   SER B 322 "
        pdb=" CA  SER B 322 "
        pdb=" C   SER B 322 "
      ideal   model   delta    sigma   weight residual
     108.24  102.24    6.00 1.32e+00 5.74e-01 2.07e+01
  ... (remaining 13427 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 5390
       17.94 -    35.88: 578
       35.88 -    53.82: 111
       53.82 -    71.76: 30
       71.76 -    89.69: 11
  Dihedral angle restraints: 6120
    sinusoidal: 2720
      harmonic: 3400
  Sorted by residual:
  dihedral pdb=" C2B HEM B 901 "
           pdb=" C3B HEM B 901 "
           pdb=" CAB HEM B 901 "
           pdb=" CBB HEM B 901 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   71.87  -71.87     2      1.00e+01 1.00e-02 4.34e+01
  dihedral pdb=" C2C HEM B 901 "
           pdb=" C3C HEM B 901 "
           pdb=" CAC HEM B 901 "
           pdb=" CBC HEM B 901 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -0.00  -65.50   65.50     2      1.00e+01 1.00e-02 3.97e+01
  dihedral pdb=" C   THR A 320 "
           pdb=" N   THR A 320 "
           pdb=" CA  THR A 320 "
           pdb=" CB  THR A 320 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -136.24   14.24     0      2.50e+00 1.60e-01 3.24e+01
  ... (remaining 6117 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.094: 1360
       0.094 -    0.187: 178
       0.187 -    0.281: 9
       0.281 -    0.375: 0
       0.375 -    0.468: 1
  Chirality restraints: 1548
  Sorted by residual:
  chirality pdb=" CA  THR A 320 "
            pdb=" N   THR A 320 "
            pdb=" C   THR A 320 "
            pdb=" CB  THR A 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.06    0.47 2.00e-01 2.50e+01 5.48e+00
  chirality pdb=" CA  PHE B 408 "
            pdb=" N   PHE B 408 "
            pdb=" C   PHE B 408 "
            pdb=" CB  PHE B 408 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" CA  THR B 320 "
            pdb=" N   THR B 320 "
            pdb=" C   THR B 320 "
            pdb=" CB  THR B 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.28    0.25 2.00e-01 2.50e+01 1.57e+00
  ... (remaining 1545 not shown)

  Planarity restraints: 1668
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG1 GSH A 901 "    0.162 2.00e-02 2.50e+03   1.94e-01 4.71e+02
        pdb=" CD1 GSH A 901 "   -0.064 2.00e-02 2.50e+03
        pdb=" OE1 GSH A 901 "   -0.009 2.00e-02 2.50e+03
        pdb=" CA2 GSH A 901 "    0.233 2.00e-02 2.50e+03
        pdb=" N2  GSH A 901 "   -0.322 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG1 GSH B 902 "    0.136 2.00e-02 2.50e+03   1.56e-01 3.05e+02
        pdb=" CD1 GSH B 902 "   -0.051 2.00e-02 2.50e+03
        pdb=" OE1 GSH B 902 "   -0.018 2.00e-02 2.50e+03
        pdb=" CA2 GSH B 902 "    0.188 2.00e-02 2.50e+03
        pdb=" N2  GSH B 902 "   -0.255 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  GSH B 902 "   -0.043 2.00e-02 2.50e+03   1.26e-01 1.97e+02
        pdb=" CA2 GSH B 902 "    0.113 2.00e-02 2.50e+03
        pdb=" CA3 GSH B 902 "    0.153 2.00e-02 2.50e+03
        pdb=" N3  GSH B 902 "   -0.201 2.00e-02 2.50e+03
        pdb=" O2  GSH B 902 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 1665 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2824
        2.82 -     3.34: 9776
        3.34 -     3.86: 15815
        3.86 -     4.38: 16675
        4.38 -     4.90: 28224
  Nonbonded interactions: 73314
  Sorted by model distance:
  nonbonded pdb=" ND1 HIS B 808 "
            pdb=" OH  TYR B 818 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" ND1 HIS A 808 "
            pdb=" OH  TYR A 818 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" NH1 ARG B 638 "
            pdb=" O   ILE B 654 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" NH1 ARG A 638 "
            pdb=" O   ILE A 654 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" OH  TYR A 424 "
            pdb=" OE1 GLN A 501 "
     model   vdw
     2.312 3.040
  ... (remaining 73309 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 236 through 826 or resid 902 or resid 904 through 905))
  selection = (chain 'B' and (resid 236 through 826 or resid 902 or resid 904 through 905))
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             1.130
  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:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     25.410
  Find NCS groups from input model:        0.650
  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:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
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      :  0.009   0.219   9874  Z= 0.442
  Angle     :  1.121   9.926  13432  Z= 0.636
  Chirality :  0.061   0.468   1548
  Planarity :  0.010   0.194   1668
  Dihedral  : 15.293  89.694   3944
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  1.10 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.09 %
  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: -0.69 (0.23), residues: 1178
  helix:  0.53 (0.18), residues: 780
  sheet: -2.29 (0.65), residues: 50
  loop : -2.39 (0.28), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 304 
 HIS   0.007   0.002   HIS A 352 
 PHE   0.050   0.004   PHE B 460 
 TYR   0.032   0.003   TYR B 466 
 ARG   0.006   0.001   ARG B 663 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14736 (  625)
  hydrogen bonds       : angle       5.57330 ( 1857)
  covalent geometry    : bond        0.00942 ( 9874)
  covalent geometry    : angle       1.12080 (13432)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 145
  time to evaluate  : 1.100 
Fit side-chains
   revert: symmetry clash
REVERT: A  275 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8517 (tm-30)
REVERT: A  408 PHE cc_start: 0.7597 (m-80) cc_final: 0.7083 (m-10)
REVERT: A  452 ARG cc_start: 0.8129 (ttm170) cc_final: 0.7864 (tpp80)
REVERT: A  614 MET cc_start: 0.8929 (mpp) cc_final: 0.8299 (mpp)
REVERT: A  748 ILE cc_start: 0.8701 (mt) cc_final: 0.8475 (mt)
REVERT: B  275 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8453 (tm-30)
REVERT: B  408 PHE cc_start: 0.7738 (m-80) cc_final: 0.7112 (m-10)
REVERT: B  452 ARG cc_start: 0.8203 (ttm170) cc_final: 0.7951 (tpp80)
REVERT: B  614 MET cc_start: 0.8889 (mpp) cc_final: 0.8231 (mpp)
REVERT: B  748 ILE cc_start: 0.8667 (mt) cc_final: 0.8430 (mt)
  outliers start: 6
  outliers final: 3
  residues processed: 147
  average time/residue: 0.1739
  time to fit residues: 38.6940
Evaluate side-chains
  95 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 92
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  455 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 99 optimal weight:    0.2980
   chunk 89 optimal weight:    2.9990
   chunk 49 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9990
   chunk 60 optimal weight:    6.9990
   chunk 47 optimal weight:    3.9990
   chunk 92 optimal weight:    6.9990
   chunk 35 optimal weight:    0.4980
   chunk 56 optimal weight:   30.0000
   chunk 68 optimal weight:    1.9990
   chunk 107 optimal weight:   10.0000
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 279 ASN
A 316 GLN
** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 539 GLN
A 557 ASN
B 279 ASN
B 316 GLN
** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 539 GLN
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.148318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.104175 restraints weight = 16379.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.107453 restraints weight = 7225.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.109603 restraints weight = 4290.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3633
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3633 r_free = 0.3633    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3630 r_free = 0.3630    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3630
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.1389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   9874  Z= 0.158
  Angle     :  0.607   9.092  13432  Z= 0.309
  Chirality :  0.039   0.139   1548
  Planarity :  0.004   0.040   1668
  Dihedral  : 10.117  88.461   1819
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 11.04 %
    Favored  : 86.55 %
  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:  0.49 (0.24), residues: 1178
  helix:  1.40 (0.18), residues: 806
  sheet: -0.12 (0.72), residues: 30
  loop : -2.33 (0.30), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 334 
 HIS   0.003   0.001   HIS A 706 
 PHE   0.016   0.001   PHE A 519 
 TYR   0.014   0.002   TYR B 465 
 ARG   0.002   0.000   ARG B 685 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06789 (  625)
  hydrogen bonds       : angle       4.48417 ( 1857)
  covalent geometry    : bond        0.00343 ( 9874)
  covalent geometry    : angle       0.60693 (13432)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 116
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8384 (tm-30)
REVERT: A  407 MET cc_start: 0.8205 (tmm) cc_final: 0.7922 (tmm)
REVERT: A  539 GLN cc_start: 0.8343 (tt0) cc_final: 0.7856 (tt0)
REVERT: A  614 MET cc_start: 0.8956 (mpp) cc_final: 0.8280 (mpp)
REVERT: A  666 ILE cc_start: 0.8891 (tp) cc_final: 0.8659 (tp)
REVERT: A  671 GLN cc_start: 0.7370 (tp-100) cc_final: 0.6812 (tp-100)
REVERT: A  748 ILE cc_start: 0.8422 (mt) cc_final: 0.8185 (mt)
REVERT: A  821 MET cc_start: 0.7979 (tmm) cc_final: 0.7770 (tmm)
REVERT: B  275 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8379 (tm-30)
REVERT: B  407 MET cc_start: 0.8122 (tmm) cc_final: 0.7862 (tmm)
REVERT: B  614 MET cc_start: 0.8976 (mpp) cc_final: 0.8294 (mpp)
REVERT: B  671 GLN cc_start: 0.7321 (tp-100) cc_final: 0.6825 (tp-100)
REVERT: B  748 ILE cc_start: 0.8467 (mt) cc_final: 0.8230 (mt)
REVERT: B  750 LEU cc_start: 0.8627 (tt) cc_final: 0.8410 (tt)
  outliers start: 24
  outliers final: 21
  residues processed: 130
  average time/residue: 0.1718
  time to fit residues: 34.0053
Evaluate side-chains
  119 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 1.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  554 ILE
Chi-restraints excluded: chain A residue  697 GLU
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  818 TYR
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  442 MET
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  554 ILE
Chi-restraints excluded: chain B residue  697 GLU
Chi-restraints excluded: chain B residue  725 LEU
Chi-restraints excluded: chain B residue  818 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 2 optimal weight:    0.0670
   chunk 10 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9990
   chunk 33 optimal weight:    7.9990
   chunk 70 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 113 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   overall best weight:    1.2124

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 HIS
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 354 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.147068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.100274 restraints weight = 17064.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.103456 restraints weight = 7768.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.105635 restraints weight = 4768.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3582
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3582 r_free = 0.3582    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3581 r_free = 0.3581    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3581
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   9874  Z= 0.142
  Angle     :  0.564   8.550  13432  Z= 0.282
  Chirality :  0.038   0.149   1548
  Planarity :  0.003   0.033   1668
  Dihedral  :  9.199  76.356   1819
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 15.96 %
    Favored  : 81.33 %
  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:  1.11 (0.25), residues: 1178
  helix:  1.89 (0.19), residues: 806
  sheet:  0.14 (0.69), residues: 34
  loop : -2.19 (0.30), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 334 
 HIS   0.003   0.001   HIS A 352 
 PHE   0.010   0.001   PHE A 533 
 TYR   0.012   0.001   TYR B 465 
 ARG   0.001   0.000   ARG A 685 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05980 (  625)
  hydrogen bonds       : angle       4.15508 ( 1857)
  covalent geometry    : bond        0.00314 ( 9874)
  covalent geometry    : angle       0.56426 (13432)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 120
  time to evaluate  : 1.081 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8346 (tm-30)
REVERT: A  338 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8224 (tm-30)
REVERT: A  539 GLN cc_start: 0.8385 (tt0) cc_final: 0.7929 (tt0)
REVERT: A  614 MET cc_start: 0.8981 (mpp) cc_final: 0.8292 (mpp)
REVERT: A  671 GLN cc_start: 0.7259 (tp-100) cc_final: 0.6995 (tp-100)
REVERT: A  705 ILE cc_start: 0.6571 (OUTLIER) cc_final: 0.6314 (mp)
REVERT: A  748 ILE cc_start: 0.8335 (mt) cc_final: 0.8124 (mt)
REVERT: B  275 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8396 (tm-30)
REVERT: B  338 GLN cc_start: 0.8966 (tm-30) cc_final: 0.8232 (tm-30)
REVERT: B  614 MET cc_start: 0.9035 (mpp) cc_final: 0.8345 (mpp)
REVERT: B  671 GLN cc_start: 0.7184 (tp-100) cc_final: 0.6933 (tp-100)
REVERT: B  705 ILE cc_start: 0.7000 (OUTLIER) cc_final: 0.6724 (mp)
REVERT: B  748 ILE cc_start: 0.8346 (mt) cc_final: 0.8138 (mt)
  outliers start: 27
  outliers final: 17
  residues processed: 137
  average time/residue: 0.1570
  time to fit residues: 33.9692
Evaluate side-chains
  121 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  554 ILE
Chi-restraints excluded: chain A residue  697 GLU
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain A residue  818 TYR
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  554 ILE
Chi-restraints excluded: chain B residue  697 GLU
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 46 optimal weight:   10.0000
   chunk 111 optimal weight:    9.9990
   chunk 51 optimal weight:    0.4980
   chunk 102 optimal weight:   20.0000
   chunk 33 optimal weight:    5.9990
   chunk 58 optimal weight:    5.9990
   chunk 61 optimal weight:    0.1980
   chunk 17 optimal weight:    1.9990
   chunk 107 optimal weight:    7.9990
   chunk 91 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 HIS
A 557 ASN
** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 354 HIS
B 652 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.147585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.102807 restraints weight = 16448.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.106020 restraints weight = 7407.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.108120 restraints weight = 4455.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3659
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3659 r_free = 0.3659    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3659 r_free = 0.3659    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3659
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.2218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9874  Z= 0.133
  Angle     :  0.566   9.576  13432  Z= 0.277
  Chirality :  0.037   0.148   1548
  Planarity :  0.003   0.030   1668
  Dihedral  :  8.406  68.722   1818
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 18.27 %
    Favored  : 78.41 %
  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:  1.36 (0.25), residues: 1178
  helix:  2.08 (0.19), residues: 810
  sheet:  0.53 (0.71), residues: 34
  loop : -2.17 (0.31), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 334 
 HIS   0.003   0.001   HIS B 808 
 PHE   0.012   0.001   PHE B 389 
 TYR   0.010   0.001   TYR A 466 
 ARG   0.002   0.000   ARG B 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05613 (  625)
  hydrogen bonds       : angle       3.99463 ( 1857)
  covalent geometry    : bond        0.00287 ( 9874)
  covalent geometry    : angle       0.56637 (13432)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 115
  time to evaluate  : 1.077 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8360 (tm-30)
REVERT: A  338 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8281 (tm-30)
REVERT: A  409 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.8373 (m-10)
REVERT: A  539 GLN cc_start: 0.8395 (tt0) cc_final: 0.7932 (tt0)
REVERT: A  614 MET cc_start: 0.8875 (mpp) cc_final: 0.8167 (mpp)
REVERT: A  637 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8224 (t80)
REVERT: A  705 ILE cc_start: 0.6583 (OUTLIER) cc_final: 0.6298 (mp)
REVERT: A  748 ILE cc_start: 0.8341 (mt) cc_final: 0.8134 (mt)
REVERT: B  275 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8319 (tm-30)
REVERT: B  315 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8503 (mp)
REVERT: B  409 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.8253 (m-10)
REVERT: B  539 GLN cc_start: 0.8471 (tt0) cc_final: 0.8003 (tt0)
REVERT: B  614 MET cc_start: 0.8946 (mpp) cc_final: 0.8228 (mpp)
REVERT: B  637 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8328 (t80)
REVERT: B  705 ILE cc_start: 0.7035 (OUTLIER) cc_final: 0.6780 (mp)
REVERT: B  748 ILE cc_start: 0.8303 (mt) cc_final: 0.8090 (mt)
REVERT: B  750 LEU cc_start: 0.8663 (tt) cc_final: 0.8400 (tt)
  outliers start: 33
  outliers final: 19
  residues processed: 140
  average time/residue: 0.1483
  time to fit residues: 33.1825
Evaluate side-chains
  128 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 102
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  409 PHE
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  554 ILE
Chi-restraints excluded: chain A residue  637 PHE
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  697 GLU
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  409 PHE
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  554 ILE
Chi-restraints excluded: chain B residue  637 PHE
Chi-restraints excluded: chain B residue  668 VAL
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  697 GLU
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 54 optimal weight:    0.0010
   chunk 65 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 105 optimal weight:   10.0000
   chunk 43 optimal weight:    4.9990
   chunk 96 optimal weight:    4.9990
   chunk 74 optimal weight:    0.8980
   chunk 59 optimal weight:   30.0000
   chunk 94 optimal weight:    3.9990
   chunk 46 optimal weight:    9.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    2.1792

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 HIS
** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 354 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.144110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.099704 restraints weight = 16626.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.102740 restraints weight = 7525.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.104751 restraints weight = 4560.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3612
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3612 r_free = 0.3612    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3612 r_free = 0.3612    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3612
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9874  Z= 0.186
  Angle     :  0.641  12.280  13432  Z= 0.305
  Chirality :  0.039   0.146   1548
  Planarity :  0.003   0.029   1668
  Dihedral  :  8.154  70.891   1818
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 18.57 %
    Favored  : 77.31 %
  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:  1.36 (0.25), residues: 1178
  helix:  2.04 (0.19), residues: 812
  sheet:  0.62 (0.70), residues: 34
  loop : -2.11 (0.31), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 334 
 HIS   0.004   0.001   HIS B 352 
 PHE   0.011   0.001   PHE B 389 
 TYR   0.015   0.001   TYR A 465 
 ARG   0.003   0.000   ARG B 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06152 (  625)
  hydrogen bonds       : angle       4.11428 ( 1857)
  covalent geometry    : bond        0.00429 ( 9874)
  covalent geometry    : angle       0.64114 (13432)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 98
  time to evaluate  : 1.041 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8341 (tm-30)
REVERT: A  539 GLN cc_start: 0.8464 (tt0) cc_final: 0.7984 (tt0)
REVERT: A  614 MET cc_start: 0.8924 (mpp) cc_final: 0.8183 (mpp)
REVERT: A  637 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8488 (t80)
REVERT: A  705 ILE cc_start: 0.6599 (OUTLIER) cc_final: 0.6288 (mp)
REVERT: A  748 ILE cc_start: 0.8421 (mt) cc_final: 0.8203 (mt)
REVERT: B  275 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8320 (tm-30)
REVERT: B  279 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8523 (t0)
REVERT: B  539 GLN cc_start: 0.8471 (tt0) cc_final: 0.8045 (tt0)
REVERT: B  614 MET cc_start: 0.8958 (mpp) cc_final: 0.8207 (mpp)
REVERT: B  637 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8414 (t80)
REVERT: B  671 GLN cc_start: 0.7108 (tp-100) cc_final: 0.6906 (tp-100)
REVERT: B  705 ILE cc_start: 0.6907 (OUTLIER) cc_final: 0.6603 (mp)
REVERT: B  748 ILE cc_start: 0.8374 (mt) cc_final: 0.8142 (mt)
REVERT: B  750 LEU cc_start: 0.8831 (tt) cc_final: 0.8475 (tt)
  outliers start: 41
  outliers final: 30
  residues processed: 133
  average time/residue: 0.1458
  time to fit residues: 30.9870
Evaluate side-chains
  128 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 93
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  554 ILE
Chi-restraints excluded: chain A residue  637 PHE
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  697 GLU
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  279 ASN
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  354 HIS
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  481 ILE
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  554 ILE
Chi-restraints excluded: chain B residue  590 ILE
Chi-restraints excluded: chain B residue  637 PHE
Chi-restraints excluded: chain B residue  668 VAL
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  697 GLU
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 110 optimal weight:    6.9990
   chunk 97 optimal weight:    6.9990
   chunk 36 optimal weight:    9.9990
   chunk 82 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 59 optimal weight:   30.0000
   chunk 50 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 HIS
** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 354 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.142198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.096106 restraints weight = 18218.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.099378 restraints weight = 8010.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.101510 restraints weight = 4842.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3569
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3569 r_free = 0.3569    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3569 r_free = 0.3569    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3569
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.2388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9874  Z= 0.141
  Angle     :  0.607  12.651  13432  Z= 0.283
  Chirality :  0.038   0.151   1548
  Planarity :  0.003   0.024   1668
  Dihedral  :  7.935  72.584   1818
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 20.88 %
    Favored  : 75.50 %
  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:  1.52 (0.25), residues: 1178
  helix:  2.17 (0.19), residues: 812
  sheet:  0.73 (0.70), residues: 34
  loop : -2.07 (0.31), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 334 
 HIS   0.006   0.001   HIS B 354 
 PHE   0.013   0.001   PHE B 408 
 TYR   0.013   0.001   TYR A 465 
 ARG   0.002   0.000   ARG B 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05771 (  625)
  hydrogen bonds       : angle       3.96698 ( 1857)
  covalent geometry    : bond        0.00312 ( 9874)
  covalent geometry    : angle       0.60748 (13432)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 101
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8307 (tm-30)
REVERT: A  614 MET cc_start: 0.8978 (mpp) cc_final: 0.8754 (mmm)
REVERT: A  637 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8337 (t80)
REVERT: A  705 ILE cc_start: 0.6707 (OUTLIER) cc_final: 0.6445 (mp)
REVERT: A  748 ILE cc_start: 0.8309 (mt) cc_final: 0.8104 (mt)
REVERT: B  275 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8330 (tm-30)
REVERT: B  539 GLN cc_start: 0.8434 (tt0) cc_final: 0.8176 (tt0)
REVERT: B  614 MET cc_start: 0.8990 (mpp) cc_final: 0.8229 (mpp)
REVERT: B  637 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8327 (t80)
REVERT: B  705 ILE cc_start: 0.6991 (OUTLIER) cc_final: 0.6745 (mp)
REVERT: B  748 ILE cc_start: 0.8244 (mt) cc_final: 0.8038 (mt)
REVERT: B  750 LEU cc_start: 0.8768 (tt) cc_final: 0.8379 (tt)
  outliers start: 36
  outliers final: 24
  residues processed: 131
  average time/residue: 0.1574
  time to fit residues: 32.7622
Evaluate side-chains
  126 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 98
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  354 HIS
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  554 ILE
Chi-restraints excluded: chain A residue  637 PHE
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  697 GLU
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain A residue  818 TYR
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  554 ILE
Chi-restraints excluded: chain B residue  590 ILE
Chi-restraints excluded: chain B residue  637 PHE
Chi-restraints excluded: chain B residue  668 VAL
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  697 GLU
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 13 optimal weight:    5.9990
   chunk 34 optimal weight:    0.1980
   chunk 11 optimal weight:    0.5980
   chunk 104 optimal weight:   10.0000
   chunk 55 optimal weight:   30.0000
   chunk 47 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 95 optimal weight:   10.0000
   chunk 60 optimal weight:   10.0000
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.147998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.103396 restraints weight = 16615.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.106649 restraints weight = 7331.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.108791 restraints weight = 4366.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3677
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3677 r_free = 0.3677    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3677 r_free = 0.3677    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3677
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.2618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9874  Z= 0.122
  Angle     :  0.592  11.542  13432  Z= 0.278
  Chirality :  0.037   0.151   1548
  Planarity :  0.003   0.026   1668
  Dihedral  :  7.755  75.118   1818
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 21.59 %
    Favored  : 74.90 %
  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:  1.67 (0.25), residues: 1178
  helix:  2.27 (0.19), residues: 812
  sheet:  0.86 (0.74), residues: 34
  loop : -1.97 (0.31), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 334 
 HIS   0.010   0.001   HIS A 354 
 PHE   0.013   0.001   PHE A 408 
 TYR   0.011   0.001   TYR A 476 
 ARG   0.001   0.000   ARG B 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05305 (  625)
  hydrogen bonds       : angle       3.82332 ( 1857)
  covalent geometry    : bond        0.00249 ( 9874)
  covalent geometry    : angle       0.59181 (13432)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 112
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8407 (tm-30)
REVERT: A  637 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8329 (t80)
REVERT: A  705 ILE cc_start: 0.6696 (OUTLIER) cc_final: 0.6429 (mp)
REVERT: B  275 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8428 (tm-30)
REVERT: B  465 TYR cc_start: 0.8945 (m-80) cc_final: 0.8694 (m-80)
REVERT: B  539 GLN cc_start: 0.8343 (tt0) cc_final: 0.7851 (tt0)
REVERT: B  637 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8298 (t80)
REVERT: B  705 ILE cc_start: 0.6912 (OUTLIER) cc_final: 0.6678 (mp)
REVERT: B  748 ILE cc_start: 0.8273 (mt) cc_final: 0.8068 (mt)
REVERT: B  750 LEU cc_start: 0.8836 (tt) cc_final: 0.8439 (tt)
  outliers start: 35
  outliers final: 23
  residues processed: 137
  average time/residue: 0.1529
  time to fit residues: 33.2267
Evaluate side-chains
  130 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 103
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  554 ILE
Chi-restraints excluded: chain A residue  637 PHE
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  697 GLU
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain A residue  818 TYR
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  554 ILE
Chi-restraints excluded: chain B residue  590 ILE
Chi-restraints excluded: chain B residue  637 PHE
Chi-restraints excluded: chain B residue  668 VAL
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  697 GLU
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 40 optimal weight:    6.9990
   chunk 43 optimal weight:    0.0770
   chunk 67 optimal weight:    6.9990
   chunk 45 optimal weight:    5.9990
   chunk 70 optimal weight:    0.6980
   chunk 49 optimal weight:    0.0270
   chunk 116 optimal weight:   10.0000
   chunk 34 optimal weight:    6.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 HIS
** B 539 GLN ** 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 = 0.4280 r_free = 0.4280 target = 0.156491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.110790 restraints weight = 16784.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.114047 restraints weight = 7328.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.116325 restraints weight = 4356.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3717
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3717 r_free = 0.3717    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3717 r_free = 0.3717    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3717
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.2926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9874  Z= 0.117
  Angle     :  0.614   9.718  13432  Z= 0.281
  Chirality :  0.037   0.144   1548
  Planarity :  0.003   0.025   1668
  Dihedral  :  7.615  79.890   1818
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 22.39 %
    Favored  : 74.20 %
  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:  1.86 (0.26), residues: 1178
  helix:  2.43 (0.19), residues: 808
  sheet:  0.94 (0.78), residues: 34
  loop : -1.92 (0.31), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 334 
 HIS   0.004   0.001   HIS B 352 
 PHE   0.012   0.001   PHE A 408 
 TYR   0.010   0.001   TYR A 476 
 ARG   0.001   0.000   ARG A 452 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04884 (  625)
  hydrogen bonds       : angle       3.72236 ( 1857)
  covalent geometry    : bond        0.00240 ( 9874)
  covalent geometry    : angle       0.61434 (13432)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 129
  time to evaluate  : 1.056 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8351 (tm-30)
REVERT: A  338 GLN cc_start: 0.8990 (tm-30) cc_final: 0.8283 (tm-30)
REVERT: A  637 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.8110 (t80)
REVERT: A  705 ILE cc_start: 0.6775 (OUTLIER) cc_final: 0.6502 (mp)
REVERT: B  275 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8363 (tm-30)
REVERT: B  465 TYR cc_start: 0.8883 (m-80) cc_final: 0.8623 (m-80)
REVERT: B  539 GLN cc_start: 0.8310 (tt0) cc_final: 0.7865 (tt0)
REVERT: B  637 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8158 (t80)
REVERT: B  686 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.8232 (t80)
REVERT: B  705 ILE cc_start: 0.7025 (OUTLIER) cc_final: 0.6820 (mp)
REVERT: B  748 ILE cc_start: 0.8142 (mt) cc_final: 0.7942 (mt)
REVERT: B  750 LEU cc_start: 0.8769 (tt) cc_final: 0.8374 (tt)
  outliers start: 34
  outliers final: 24
  residues processed: 149
  average time/residue: 0.1452
  time to fit residues: 34.4343
Evaluate side-chains
  144 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 115
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  354 HIS
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  554 ILE
Chi-restraints excluded: chain A residue  590 ILE
Chi-restraints excluded: chain A residue  637 PHE
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  697 GLU
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain A residue  818 TYR
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  519 PHE
Chi-restraints excluded: chain B residue  554 ILE
Chi-restraints excluded: chain B residue  590 ILE
Chi-restraints excluded: chain B residue  633 LEU
Chi-restraints excluded: chain B residue  637 PHE
Chi-restraints excluded: chain B residue  668 VAL
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  686 TYR
Chi-restraints excluded: chain B residue  697 GLU
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 4 optimal weight:    0.1980
   chunk 74 optimal weight:    0.0000
   chunk 52 optimal weight:    0.3980
   chunk 81 optimal weight:    1.9990
   chunk 2 optimal weight:    6.9990
   chunk 48 optimal weight:    7.9990
   chunk 43 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9990
   chunk 80 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   overall best weight:    0.4786

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 HIS
** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 683 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 = 0.4288 r_free = 0.4288 target = 0.157538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.112209 restraints weight = 16533.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.115532 restraints weight = 7226.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.117765 restraints weight = 4281.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3729
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3729 r_free = 0.3729    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3729 r_free = 0.3729    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3729
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.3116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   9874  Z= 0.117
  Angle     :  0.617   9.283  13432  Z= 0.284
  Chirality :  0.037   0.147   1548
  Planarity :  0.003   0.023   1668
  Dihedral  :  7.571  84.505   1818
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 22.59 %
    Favored  : 73.80 %
  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:  1.94 (0.26), residues: 1178
  helix:  2.49 (0.19), residues: 808
  sheet:  1.09 (0.79), residues: 34
  loop : -1.88 (0.31), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.000   TRP B 334 
 HIS   0.011   0.001   HIS A 354 
 PHE   0.019   0.001   PHE B 408 
 TYR   0.015   0.001   TYR A 476 
 ARG   0.001   0.000   ARG A 452 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04734 (  625)
  hydrogen bonds       : angle       3.70954 ( 1857)
  covalent geometry    : bond        0.00241 ( 9874)
  covalent geometry    : angle       0.61688 (13432)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 125
  time to evaluate  : 1.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8371 (tm-30)
REVERT: A  338 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8312 (tm-30)
REVERT: A  522 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8592 (tt0)
REVERT: A  539 GLN cc_start: 0.8401 (tt0) cc_final: 0.8195 (tt0)
REVERT: A  705 ILE cc_start: 0.6783 (OUTLIER) cc_final: 0.6522 (mp)
REVERT: B  275 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8388 (tm-30)
REVERT: B  465 TYR cc_start: 0.8840 (m-80) cc_final: 0.8605 (m-80)
REVERT: B  522 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8663 (tt0)
REVERT: B  539 GLN cc_start: 0.8257 (tt0) cc_final: 0.7822 (tt0)
REVERT: B  637 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.8187 (t80)
REVERT: B  686 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.8222 (t80)
REVERT: B  722 GLU cc_start: 0.8539 (tt0) cc_final: 0.8305 (pp20)
REVERT: B  750 LEU cc_start: 0.8777 (tt) cc_final: 0.8377 (tt)
  outliers start: 36
  outliers final: 25
  residues processed: 148
  average time/residue: 0.1534
  time to fit residues: 36.0302
Evaluate side-chains
  145 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 115
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  522 GLU
Chi-restraints excluded: chain A residue  554 ILE
Chi-restraints excluded: chain A residue  590 ILE
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  697 GLU
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain A residue  818 TYR
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  354 HIS
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  519 PHE
Chi-restraints excluded: chain B residue  522 GLU
Chi-restraints excluded: chain B residue  554 ILE
Chi-restraints excluded: chain B residue  590 ILE
Chi-restraints excluded: chain B residue  633 LEU
Chi-restraints excluded: chain B residue  637 PHE
Chi-restraints excluded: chain B residue  668 VAL
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  686 TYR
Chi-restraints excluded: chain B residue  697 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 48 optimal weight:    7.9990
   chunk 91 optimal weight:    0.6980
   chunk 108 optimal weight:    5.9990
   chunk 37 optimal weight:   30.0000
   chunk 84 optimal weight:    2.9990
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 652 GLN
** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 706 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.150860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.106392 restraints weight = 16594.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.109571 restraints weight = 7355.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.111695 restraints weight = 4389.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3717
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3717 r_free = 0.3717    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3717 r_free = 0.3717    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3717
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.3156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9874  Z= 0.129
  Angle     :  0.656   9.938  13432  Z= 0.301
  Chirality :  0.037   0.207   1548
  Planarity :  0.003   0.025   1668
  Dihedral  :  7.604  87.066   1818
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 23.80 %
    Favored  : 72.79 %
  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:  1.99 (0.26), residues: 1178
  helix:  2.57 (0.19), residues: 800
  sheet:  1.13 (0.80), residues: 34
  loop : -1.88 (0.31), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.000   TRP B 334 
 HIS   0.008   0.001   HIS A 706 
 PHE   0.027   0.001   PHE A 408 
 TYR   0.012   0.001   TYR A 476 
 ARG   0.002   0.000   ARG A 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04904 (  625)
  hydrogen bonds       : angle       3.72804 ( 1857)
  covalent geometry    : bond        0.00280 ( 9874)
  covalent geometry    : angle       0.65612 (13432)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 114
  time to evaluate  : 0.984 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8412 (tm-30)
REVERT: A  522 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8546 (tt0)
REVERT: A  539 GLN cc_start: 0.8428 (tt0) cc_final: 0.8225 (tt0)
REVERT: A  705 ILE cc_start: 0.6658 (OUTLIER) cc_final: 0.6420 (mp)
REVERT: B  275 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8439 (tm-30)
REVERT: B  315 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8716 (tp)
REVERT: B  522 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8683 (tt0)
REVERT: B  637 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.8253 (t80)
REVERT: B  686 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.8304 (t80)
REVERT: B  750 LEU cc_start: 0.8811 (tt) cc_final: 0.8430 (tt)
  outliers start: 34
  outliers final: 23
  residues processed: 132
  average time/residue: 0.1516
  time to fit residues: 31.6612
Evaluate side-chains
  139 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 110
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  522 GLU
Chi-restraints excluded: chain A residue  554 ILE
Chi-restraints excluded: chain A residue  590 ILE
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  697 GLU
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain A residue  818 TYR
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  519 PHE
Chi-restraints excluded: chain B residue  522 GLU
Chi-restraints excluded: chain B residue  554 ILE
Chi-restraints excluded: chain B residue  590 ILE
Chi-restraints excluded: chain B residue  633 LEU
Chi-restraints excluded: chain B residue  637 PHE
Chi-restraints excluded: chain B residue  668 VAL
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  686 TYR
Chi-restraints excluded: chain B residue  697 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 105 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 109 optimal weight:    6.9990
   chunk 74 optimal weight:    0.0670
   chunk 72 optimal weight:    0.9980
   chunk 53 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 36 optimal weight:   10.0000
   chunk 42 optimal weight:    0.5980
   chunk 69 optimal weight:    0.3980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 706 HIS ** 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 = 0.4288 r_free = 0.4288 target = 0.157154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.111465 restraints weight = 16654.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.114787 restraints weight = 7354.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.117023 restraints weight = 4372.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3727
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3727 r_free = 0.3727    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3726 r_free = 0.3726    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3726
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.3344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9874  Z= 0.122
  Angle     :  0.655   9.999  13432  Z= 0.301
  Chirality :  0.037   0.264   1548
  Planarity :  0.003   0.026   1668
  Dihedral  :  7.596  89.550   1818
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 24.50 %
    Favored  : 72.59 %
  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:  2.02 (0.25), residues: 1178
  helix:  2.53 (0.19), residues: 808
  sheet:  1.22 (0.81), residues: 34
  loop : -1.82 (0.31), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.000   TRP B 334 
 HIS   0.010   0.001   HIS A 706 
 PHE   0.016   0.001   PHE A 408 
 TYR   0.011   0.001   TYR A 476 
 ARG   0.002   0.000   ARG B 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04675 (  625)
  hydrogen bonds       : angle       3.68048 ( 1857)
  covalent geometry    : bond        0.00258 ( 9874)
  covalent geometry    : angle       0.65524 (13432)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3349.49 seconds
wall clock time: 59 minutes 6.49 seconds (3546.49 seconds total)