Starting phenix.real_space_refine
on Fri Jun 20 02:15:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f2w_50165/06_2025/9f2w_50165_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f2w_50165/06_2025/9f2w_50165.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.21
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9f2w_50165/06_2025/9f2w_50165.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f2w_50165/06_2025/9f2w_50165.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f2w_50165/06_2025/9f2w_50165_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f2w_50165/06_2025/9f2w_50165_trim.cif"
  }
  resolution = 4.21
  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=   0.000 sd=   0.001
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: 7
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P      62      5.49       5
     S      66      5.16       5
     C    7338      2.51       5
     N    2092      2.21       5
     O    2402      1.98       5
     H   11450      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 23412
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 10774
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 675, 10774
          Classifications: {'peptide': 675}
          Link IDs: {'PTRANS': 21, 'TRANS': 653}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 78
          Unresolved non-hydrogen angles: 91
          Unresolved non-hydrogen dihedrals: 68
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 41
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' ZN': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 459
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 459
          Classifications: {'RNA': 14}
          Modifications used: {'3*END': 1, 'rna3p_pur': 10, 'rna3p_pyr': 4}
          Link IDs: {'rna3p': 13}
    Chain: "D"
      Number of atoms: 441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 441
          Classifications: {'RNA': 14}
          Modifications used: {'3*END': 1, 'rna3p_pur': 4, 'rna3p_pyr': 10}
          Link IDs: {'rna3p': 13}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   9106  SG  CYS A 907      78.024  41.491  84.218  1.00169.40           S
  ATOM   9152  SG  CYS A 910      81.747  41.327  84.273  1.00177.05           S
  ATOM   9797  SG  CYS A 962      79.858  42.092  87.525  1.00171.25           S
  ATOM   9829  SG  CYS A 964      80.088  44.703  84.968  1.00176.38           S

  Restraints were copied for chains:
    Y, X, B
  Time building chain proxies: 33.61, per 1000 atoms: 1.44
  Number of scatterers: 23412
  At special positions: 0
  Unit cell: (102.424, 94.99, 118.944, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      2     29.99
     S      66     16.00
     P      62     15.00
     O    2402      8.00
     N    2092      7.00
     C    7338      6.00
     H   11450      1.00
    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: 6.44
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1101 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 962 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 964 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 910 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 907 "
      pdb="  ZN B1101 "
        pdb="ZN    ZN B1101 " - pdb=" SG  CYS B 962 "
        pdb="ZN    ZN B1101 " - pdb=" SG  CYS B 964 "
        pdb="ZN    ZN B1101 " - pdb=" SG  CYS B 910 "
        pdb="ZN    ZN B1101 " - pdb=" SG  CYS B 907 "
      Number of angles added : 12


  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2580

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 10 sheets defined
      57.0% alpha, 11.0% beta
      28 base pairs and 30 stacking pairs defined.
    Time for finding SS restraints: 10.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 310 through 318
    Processing helix  chain 'A' and resid 319 through 322
    Processing helix  chain 'A' and resid 335 through 354
    Processing helix  chain 'A' and resid 366 through 377
      removed outlier: 3.933A  pdb=" N   ALA A 370 " --> pdb=" O   LYS A 366 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLU A 371 " --> pdb=" O   VAL A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 383
    Processing helix  chain 'A' and resid 400 through 409
      removed outlier: 3.774A  pdb=" N   VAL A 404 " --> pdb=" O   SER A 400 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   LYS A 406 " --> pdb=" O   PRO A 402 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   TYR A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   ASP A 409 " --> pdb=" O   VAL A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 428
    Processing helix  chain 'A' and resid 434 through 438
    Processing helix  chain 'A' and resid 446 through 449
    Processing helix  chain 'A' and resid 453 through 476
    Processing helix  chain 'A' and resid 499 through 515
    Processing helix  chain 'A' and resid 525 through 533
    Processing helix  chain 'A' and resid 548 through 567
    Processing helix  chain 'A' and resid 576 through 594
    Processing helix  chain 'A' and resid 599 through 616
    Processing helix  chain 'A' and resid 619 through 645
      removed outlier: 3.791A  pdb=" N   ALA A 623 " --> pdb=" O   ARG A 619 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 671 through 693
      removed outlier: 4.529A  pdb=" N   LYS A 685 " --> pdb=" O   PHE A 681 " (cutoff:3.500A)
      removed outlier: 5.073A  pdb=" N   MET A 686 " --> pdb=" O   ASP A 682 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ASN A 693 " --> pdb=" O   LYS A 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 700 through 716
    Processing helix  chain 'A' and resid 727 through 741
    Processing helix  chain 'A' and resid 741 through 748
      removed outlier: 3.893A  pdb=" N   ALA A 745 " --> pdb=" O   ASN A 741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 767 through 781
    Processing helix  chain 'A' and resid 789 through 794
      removed outlier: 3.776A  pdb=" N   GLU A 793 " --> pdb=" O   THR A 789 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   GLU A 794 " --> pdb=" O   THR A 790 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 789 through 794'
    Processing helix  chain 'A' and resid 812 through 822
    Processing helix  chain 'A' and resid 840 through 863
      removed outlier: 3.696A  pdb=" N   ARG A 860 " --> pdb=" O   LYS A 856 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 895
      removed outlier: 3.742A  pdb=" N   GLN A 895 " --> pdb=" O   SER A 891 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 932 through 937
      removed outlier: 3.518A  pdb=" N   LYS A 936 " --> pdb=" O   THR A 932 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 984 through 987
    Processing helix  chain 'A' and resid 1014 through 1019
    Processing helix  chain 'B' and resid 310 through 318
    Processing helix  chain 'B' and resid 319 through 322
    Processing helix  chain 'B' and resid 335 through 354
    Processing helix  chain 'B' and resid 366 through 377
      removed outlier: 3.933A  pdb=" N   ALA B 370 " --> pdb=" O   LYS B 366 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLU B 371 " --> pdb=" O   VAL B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 377 through 383
    Processing helix  chain 'B' and resid 400 through 409
      removed outlier: 3.774A  pdb=" N   VAL B 404 " --> pdb=" O   SER B 400 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   LYS B 406 " --> pdb=" O   PRO B 402 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   TYR B 408 " --> pdb=" O   VAL B 404 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   ASP B 409 " --> pdb=" O   VAL B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 415 through 428
    Processing helix  chain 'B' and resid 434 through 438
    Processing helix  chain 'B' and resid 446 through 449
    Processing helix  chain 'B' and resid 453 through 476
    Processing helix  chain 'B' and resid 499 through 515
    Processing helix  chain 'B' and resid 525 through 533
    Processing helix  chain 'B' and resid 548 through 567
    Processing helix  chain 'B' and resid 576 through 594
    Processing helix  chain 'B' and resid 599 through 616
    Processing helix  chain 'B' and resid 619 through 645
      removed outlier: 3.791A  pdb=" N   ALA B 623 " --> pdb=" O   ARG B 619 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 671 through 693
      removed outlier: 4.530A  pdb=" N   LYS B 685 " --> pdb=" O   PHE B 681 " (cutoff:3.500A)
      removed outlier: 5.073A  pdb=" N   MET B 686 " --> pdb=" O   ASP B 682 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ASN B 693 " --> pdb=" O   LYS B 689 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 700 through 716
    Processing helix  chain 'B' and resid 727 through 741
    Processing helix  chain 'B' and resid 741 through 748
      removed outlier: 3.893A  pdb=" N   ALA B 745 " --> pdb=" O   ASN B 741 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 767 through 781
    Processing helix  chain 'B' and resid 789 through 794
      removed outlier: 3.776A  pdb=" N   GLU B 793 " --> pdb=" O   THR B 789 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLU B 794 " --> pdb=" O   THR B 790 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 789 through 794'
    Processing helix  chain 'B' and resid 812 through 822
    Processing helix  chain 'B' and resid 840 through 863
      removed outlier: 3.697A  pdb=" N   ARG B 860 " --> pdb=" O   LYS B 856 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 865 through 895
      removed outlier: 3.742A  pdb=" N   GLN B 895 " --> pdb=" O   SER B 891 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 932 through 937
      removed outlier: 3.518A  pdb=" N   LYS B 936 " --> pdb=" O   THR B 932 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 984 through 987
    Processing helix  chain 'B' and resid 1014 through 1019
    Processing sheet with id=1, first strand: chain 'A' and resid 327 through 329
      removed outlier: 5.943A  pdb=" N   ILE A 328 " --> pdb=" O   THR A 489 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   ILE A 361 " --> pdb=" O   ILE A 442 " (cutoff:3.500A)
      removed outlier: 7.800A  pdb=" N   ASP A 444 " --> pdb=" O   ILE A 361 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   LEU A 363 " --> pdb=" O   ASP A 444 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   VAL A 360 " --> pdb=" O   ILE A 411 " (cutoff:3.500A)
      removed outlier: 7.825A  pdb=" N   SER A 413 " --> pdb=" O   VAL A 360 " (cutoff:3.500A)
      removed outlier: 5.632A  pdb=" N   VAL A 362 " --> pdb=" O   SER A 413 " (cutoff:3.500A)
    Processing sheet with id=2, first strand: chain 'A' and resid 537 through 541
      removed outlier: 5.584A  pdb=" N   CYS A 537 " --> pdb=" O   TYR A 830 " (cutoff:3.500A)
      removed outlier: 7.359A  pdb=" N   LEU A 832 " --> pdb=" O   CYS A 537 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   LYS A 539 " --> pdb=" O   LEU A 832 " (cutoff:3.500A)
      removed outlier: 5.453A  pdb=" N   ASN A 802 " --> pdb=" O   GLU A 827 " (cutoff:3.500A)
      removed outlier: 5.542A  pdb=" N   ILE A 722 " --> pdb=" O   ILE A 805 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   TYR A 807 " --> pdb=" O   ILE A 722 " (cutoff:3.500A)
      removed outlier: 5.819A  pdb=" N   PHE A 724 " --> pdb=" O   TYR A 807 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   GLY A 721 " --> pdb=" O   LEU A 786 " (cutoff:3.500A)
      removed outlier: 7.270A  pdb=" N   ALA A 788 " --> pdb=" O   GLY A 721 " (cutoff:3.500A)
      removed outlier: 5.538A  pdb=" N   ILE A 723 " --> pdb=" O   ALA A 788 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   HIS A 752 " --> pdb=" O   ILE A 787 " (cutoff:3.500A)
    Processing sheet with id=3, first strand: chain 'A' and resid 913 through 915
    Processing sheet with id=4, first strand: chain 'A' and resid 920 through 923
    Processing sheet with id=5, first strand: chain 'A' and resid 940 through 942
      removed outlier: 3.892A  pdb=" N   GLY A 969 " --> pdb=" O   ILE A 960 " (cutoff:3.500A)
    Processing sheet with id=6, first strand: chain 'B' and resid 327 through 329
      removed outlier: 5.942A  pdb=" N   ILE B 328 " --> pdb=" O   THR B 489 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   ILE B 361 " --> pdb=" O   ILE B 442 " (cutoff:3.500A)
      removed outlier: 7.800A  pdb=" N   ASP B 444 " --> pdb=" O   ILE B 361 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   LEU B 363 " --> pdb=" O   ASP B 444 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   VAL B 360 " --> pdb=" O   ILE B 411 " (cutoff:3.500A)
      removed outlier: 7.824A  pdb=" N   SER B 413 " --> pdb=" O   VAL B 360 " (cutoff:3.500A)
      removed outlier: 5.633A  pdb=" N   VAL B 362 " --> pdb=" O   SER B 413 " (cutoff:3.500A)
    Processing sheet with id=7, first strand: chain 'B' and resid 537 through 541
      removed outlier: 5.584A  pdb=" N   CYS B 537 " --> pdb=" O   TYR B 830 " (cutoff:3.500A)
      removed outlier: 7.358A  pdb=" N   LEU B 832 " --> pdb=" O   CYS B 537 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   LYS B 539 " --> pdb=" O   LEU B 832 " (cutoff:3.500A)
      removed outlier: 5.453A  pdb=" N   ASN B 802 " --> pdb=" O   GLU B 827 " (cutoff:3.500A)
      removed outlier: 5.542A  pdb=" N   ILE B 722 " --> pdb=" O   ILE B 805 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   TYR B 807 " --> pdb=" O   ILE B 722 " (cutoff:3.500A)
      removed outlier: 5.819A  pdb=" N   PHE B 724 " --> pdb=" O   TYR B 807 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   GLY B 721 " --> pdb=" O   LEU B 786 " (cutoff:3.500A)
      removed outlier: 7.270A  pdb=" N   ALA B 788 " --> pdb=" O   GLY B 721 " (cutoff:3.500A)
      removed outlier: 5.539A  pdb=" N   ILE B 723 " --> pdb=" O   ALA B 788 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   HIS B 752 " --> pdb=" O   ILE B 787 " (cutoff:3.500A)
    Processing sheet with id=8, first strand: chain 'B' and resid 913 through 915
    Processing sheet with id=9, first strand: chain 'B' and resid 920 through 923
    Processing sheet with id=10, first strand: chain 'B' and resid 940 through 942
      removed outlier: 3.891A  pdb=" N   GLY B 969 " --> pdb=" O   ILE B 960 " (cutoff:3.500A)

    584 hydrogen bonds defined for protein.
    1674 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      72 hydrogen bonds
      144 hydrogen bond angles
      0 basepair planarities
      28 basepair parallelities
      30 stacking parallelities
  Total time for adding SS restraints: 9.00

  Time building geometry restraints manager: 7.69 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 11430
        1.03 -     1.23: 36
        1.23 -     1.42: 5106
        1.42 -     1.62: 7044
        1.62 -     1.81: 104
  Bond restraints: 23720
  Sorted by residual:
  bond pdb=" CA  HIS B 974 "
       pdb=" CB  HIS B 974 "
    ideal  model  delta    sigma   weight residual
    1.532  1.495  0.037 1.58e-02 4.01e+03 5.53e+00
  bond pdb=" CA  HIS A 974 "
       pdb=" CB  HIS A 974 "
    ideal  model  delta    sigma   weight residual
    1.532  1.495  0.037 1.58e-02 4.01e+03 5.40e+00
  bond pdb=" CB  HIS A 974 "
       pdb=" CG  HIS A 974 "
    ideal  model  delta    sigma   weight residual
    1.497  1.468  0.029 1.40e-02 5.10e+03 4.19e+00
  bond pdb=" CB  HIS B 974 "
       pdb=" CG  HIS B 974 "
    ideal  model  delta    sigma   weight residual
    1.497  1.469  0.028 1.40e-02 5.10e+03 4.02e+00
  bond pdb=" N   HIS A 974 "
       pdb=" CA  HIS A 974 "
    ideal  model  delta    sigma   weight residual
    1.458  1.439  0.019 1.19e-02 7.06e+03 2.56e+00
  ... (remaining 23715 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 41402
        1.32 -     2.65: 1377
        2.65 -     3.97: 169
        3.97 -     5.29: 16
        5.29 -     6.62: 8
  Bond angle restraints: 42972
  Sorted by residual:
  angle pdb=" C3' ATP A1102 "
        pdb=" C4' ATP A1102 "
        pdb=" C5' ATP A1102 "
      ideal   model   delta    sigma   weight residual
     115.19  110.57    4.62 1.76e+00 3.23e-01 6.88e+00
  angle pdb=" C3' ATP B1102 "
        pdb=" C4' ATP B1102 "
        pdb=" C5' ATP B1102 "
      ideal   model   delta    sigma   weight residual
     115.19  110.59    4.60 1.76e+00 3.23e-01 6.84e+00
  angle pdb=" C   LYS A 772 "
        pdb=" N   GLU A 773 "
        pdb=" CA  GLU A 773 "
      ideal   model   delta    sigma   weight residual
     120.31  116.57    3.74 1.52e+00 4.33e-01 6.05e+00
  angle pdb=" C   LYS B 772 "
        pdb=" N   GLU B 773 "
        pdb=" CA  GLU B 773 "
      ideal   model   delta    sigma   weight residual
     120.31  116.59    3.72 1.52e+00 4.33e-01 6.00e+00
  angle pdb=" C1' ATP A1102 "
        pdb=" C2' ATP A1102 "
        pdb=" O2' ATP A1102 "
      ideal   model   delta    sigma   weight residual
     110.58  103.96    6.62 2.79e+00 1.28e-01 5.61e+00
  ... (remaining 42967 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 10102
       17.88 -    35.75: 712
       35.75 -    53.63: 230
       53.63 -    71.50: 98
       71.50 -    89.38: 26
  Dihedral angle restraints: 11168
    sinusoidal: 6662
      harmonic: 4506
  Sorted by residual:
  dihedral pdb=" CA  LEU A 397 "
           pdb=" C   LEU A 397 "
           pdb=" N   LYS A 398 "
           pdb=" CA  LYS A 398 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.96  -23.04     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  LEU B 397 "
           pdb=" C   LEU B 397 "
           pdb=" N   LYS B 398 "
           pdb=" CA  LYS B 398 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.98  -23.02     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CB  GLU B 356 "
           pdb=" CG  GLU B 356 "
           pdb=" CD  GLU B 356 "
           pdb=" OE1 GLU B 356 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.38  -89.38     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 11165 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1714
       0.055 -    0.110: 193
       0.110 -    0.165: 41
       0.165 -    0.220: 0
       0.220 -    0.276: 6
  Chirality restraints: 1954
  Sorted by residual:
  chirality pdb=" C3' ATP B1102 "
            pdb=" C2' ATP B1102 "
            pdb=" C4' ATP B1102 "
            pdb=" O3' ATP B1102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.91    0.28 2.00e-01 2.50e+01 1.90e+00
  chirality pdb=" C3' ATP A1102 "
            pdb=" C2' ATP A1102 "
            pdb=" C4' ATP A1102 "
            pdb=" O3' ATP A1102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.91    0.28 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" C2' ATP B1102 "
            pdb=" C1' ATP B1102 "
            pdb=" C3' ATP B1102 "
            pdb=" O2' ATP B1102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.95    0.27 2.00e-01 2.50e+01 1.85e+00
  ... (remaining 1951 not shown)

  Planarity restraints: 3266
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 569 "   -0.028 5.00e-02 4.00e+02   4.16e-02 2.77e+00
        pdb=" N   PRO A 570 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A 570 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 570 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 569 "   -0.027 5.00e-02 4.00e+02   4.14e-02 2.74e+00
        pdb=" N   PRO B 570 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO B 570 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 570 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS B 974 "   -0.007 2.00e-02 2.50e+03   1.48e-02 2.18e+00
        pdb=" C   HIS B 974 "    0.026 2.00e-02 2.50e+03
        pdb=" O   HIS B 974 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   LYS B 975 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 3263 not shown)

  Histogram of nonbonded interaction distances:
        1.20 -     1.88: 111
        1.88 -     2.56: 22059
        2.56 -     3.24: 72880
        3.24 -     3.92: 88841
        3.92 -     4.60: 138947
  Nonbonded interactions: 322838
  Sorted by model distance:
  nonbonded pdb="HH22 ARG A 890 "
            pdb=" O   GLY B 976 "
     model   vdw
     1.196 2.450
  nonbonded pdb=" HE2 HIS B 927 "
            pdb=" O2'   G C   4 "
     model   vdw
     1.517 2.450
  nonbonded pdb=" HE2 HIS A 927 "
            pdb=" O2'   G X   4 "
     model   vdw
     1.517 2.450
  nonbonded pdb=" HZ1 LYS A1001 "
            pdb=" OP1   U Y   4 "
     model   vdw
     1.541 2.450
  nonbonded pdb=" HZ1 LYS B1001 "
            pdb=" OP1   U D   4 "
     model   vdw
     1.541 2.450
  ... (remaining 322833 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'D'
  selection = chain 'Y'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'X'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.380
  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:             0.380
  Extract box with map and model:          0.920
  Check model and map are aligned:         0.180
  Set scattering table:                    0.240
  Process input model:                     89.910
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.060
  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:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   96.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12278  Z= 0.167
  Angle     :  0.574   6.618  16816  Z= 0.306
  Chirality :  0.041   0.276   1954
  Planarity :  0.003   0.042   1924
  Dihedral  : 15.378  89.380   5092
  Min Nonbonded Distance : 1.696

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  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: -0.24 (0.23), residues: 1330
  helix:  1.47 (0.20), residues: 670
  sheet: -1.13 (0.42), residues: 164
  loop : -2.16 (0.25), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 385 
 HIS   0.007   0.001   HIS B 974 
 PHE   0.014   0.001   PHE A 680 
 TYR   0.007   0.001   TYR A 342 
 ARG   0.005   0.001   ARG B 705 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13111 (  656)
  hydrogen bonds       : angle       5.56894 ( 1818)
  metal coordination   : bond        0.00595 (    8)
  metal coordination   : angle       3.21944 (   12)
  covalent geometry    : bond        0.00330 (12270)
  covalent geometry    : angle       0.56728 (16804)

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  352 is missing expected H atoms. Skipping.
Residue THR  546 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  597 is missing expected H atoms. Skipping.
Residue TYR  608 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  750 is missing expected H atoms. Skipping.
Residue MET  816 is missing expected H atoms. Skipping.
Residue LYS  894 is missing expected H atoms. Skipping.
Residue MET  931 is missing expected H atoms. Skipping.
Residue LYS  352 is missing expected H atoms. Skipping.
Residue THR  546 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  597 is missing expected H atoms. Skipping.
Residue TYR  608 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  750 is missing expected H atoms. Skipping.
Residue MET  816 is missing expected H atoms. Skipping.
Residue LYS  894 is missing expected H atoms. Skipping.
Residue MET  931 is missing expected H atoms. Skipping.
Evaluate side-chains
  235 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 1.762 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  377 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6726 (mm-30)
REVERT: A  586 MET cc_start: 0.8496 (tpp) cc_final: 0.8163 (tpp)
REVERT: A  599 ARG cc_start: 0.6701 (ptp-170) cc_final: 0.5717 (mtm110)
REVERT: A  610 GLU cc_start: 0.8702 (pp20) cc_final: 0.8478 (pp20)
REVERT: A  677 MET cc_start: 0.6584 (ptm) cc_final: 0.6329 (ptm)
REVERT: A  918 GLU cc_start: 0.7680 (pm20) cc_final: 0.7072 (pm20)
REVERT: B  759 HIS cc_start: 0.5698 (p-80) cc_final: 0.5485 (t70)
REVERT: B  999 GLN cc_start: 0.8213 (tt0) cc_final: 0.7457 (mm-40)
  outliers start: 0
  outliers final: 0
  residues processed: 235
  average time/residue: 0.5279
  time to fit residues: 176.6992
Evaluate side-chains
  160 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 1.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 116 optimal weight:    9.9990
   chunk 104 optimal weight:    5.9990
   chunk 58 optimal weight:    9.9990
   chunk 35 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 55 optimal weight:    8.9990
   chunk 108 optimal weight:    0.6980
   chunk 41 optimal weight:    6.9990
   chunk 65 optimal weight:    5.9990
   chunk 80 optimal weight:    3.9990
   chunk 125 optimal weight:    4.9990
   overall best weight:    3.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 313 GLN
A 416 GLN
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 879 GLN
B 416 GLN
** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 919 ASN
B 974 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.093706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.071119 restraints weight = 115289.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.074758 restraints weight = 49684.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.077051 restraints weight = 30043.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12278  Z= 0.202
  Angle     :  0.606   5.404  16816  Z= 0.327
  Chirality :  0.040   0.153   1954
  Planarity :  0.004   0.062   1924
  Dihedral  : 14.388  81.841   2374
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  2.73 %
    Favored  : 96.93 %
  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: -0.33 (0.23), residues: 1330
  helix:  1.36 (0.19), residues: 700
  sheet: -1.24 (0.40), residues: 174
  loop : -2.36 (0.25), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 582 
 HIS   0.009   0.002   HIS A 531 
 PHE   0.012   0.002   PHE A 680 
 TYR   0.019   0.002   TYR B 408 
 ARG   0.005   0.001   ARG A 468 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04587 (  656)
  hydrogen bonds       : angle       4.70561 ( 1818)
  metal coordination   : bond        0.00841 (    8)
  metal coordination   : angle       2.64271 (   12)
  covalent geometry    : bond        0.00407 (12270)
  covalent geometry    : angle       0.60233 (16804)

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  352 is missing expected H atoms. Skipping.
Residue THR  546 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  597 is missing expected H atoms. Skipping.
Residue TYR  608 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  750 is missing expected H atoms. Skipping.
Residue MET  816 is missing expected H atoms. Skipping.
Residue LYS  894 is missing expected H atoms. Skipping.
Residue MET  931 is missing expected H atoms. Skipping.
Residue LYS  352 is missing expected H atoms. Skipping.
Residue THR  546 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  597 is missing expected H atoms. Skipping.
Residue TYR  608 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  750 is missing expected H atoms. Skipping.
Residue MET  816 is missing expected H atoms. Skipping.
Residue LYS  894 is missing expected H atoms. Skipping.
Residue MET  931 is missing expected H atoms. Skipping.
Evaluate side-chains
  194 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 190
  time to evaluate  : 1.953 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  377 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7476 (mm-30)
REVERT: A  918 GLU cc_start: 0.7747 (pm20) cc_final: 0.7545 (pm20)
REVERT: B  520 LYS cc_start: 0.8663 (mmmt) cc_final: 0.8438 (mmmm)
REVERT: B  807 TYR cc_start: 0.7834 (t80) cc_final: 0.7479 (t80)
REVERT: B  886 MET cc_start: 0.8496 (mtm) cc_final: 0.8215 (mtm)
REVERT: B  926 MET cc_start: 0.8789 (ptp) cc_final: 0.8468 (ptp)
  outliers start: 4
  outliers final: 2
  residues processed: 193
  average time/residue: 0.4817
  time to fit residues: 137.9594
Evaluate side-chains
  145 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 143
  time to evaluate  : 1.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 119 optimal weight:   20.0000
   chunk 40 optimal weight:   10.0000
   chunk 129 optimal weight:    8.9990
   chunk 54 optimal weight:    8.9990
   chunk 22 optimal weight:    0.7980
   chunk 85 optimal weight:    8.9990
   chunk 47 optimal weight:    6.9990
   chunk 7 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 98 optimal weight:    8.9990
   overall best weight:    5.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 416 GLN
A 475 GLN
A 484 GLN
A 525 ASN
** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 416 GLN
B 447 HIS
B 470 ASN
B 475 GLN
B 525 ASN
** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 919 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.089525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.066708 restraints weight = 119106.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.070196 restraints weight = 50202.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.072382 restraints weight = 30844.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.3947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  12278  Z= 0.266
  Angle     :  0.673   6.800  16816  Z= 0.363
  Chirality :  0.042   0.182   1954
  Planarity :  0.005   0.044   1924
  Dihedral  : 14.990  81.598   2374
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  4.44 %
    Favored  : 95.31 %
  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: -0.89 (0.22), residues: 1330
  helix:  1.00 (0.19), residues: 714
  sheet: -1.72 (0.38), residues: 164
  loop : -2.79 (0.24), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B1003 
 HIS   0.008   0.002   HIS A 927 
 PHE   0.018   0.002   PHE A 675 
 TYR   0.022   0.002   TYR B 408 
 ARG   0.011   0.001   ARG A 890 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05186 (  656)
  hydrogen bonds       : angle       4.81807 ( 1818)
  metal coordination   : bond        0.01337 (    8)
  metal coordination   : angle       2.61719 (   12)
  covalent geometry    : bond        0.00545 (12270)
  covalent geometry    : angle       0.66929 (16804)

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  352 is missing expected H atoms. Skipping.
Residue THR  546 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  597 is missing expected H atoms. Skipping.
Residue TYR  608 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  750 is missing expected H atoms. Skipping.
Residue MET  816 is missing expected H atoms. Skipping.
Residue LYS  894 is missing expected H atoms. Skipping.
Residue MET  931 is missing expected H atoms. Skipping.
Residue LYS  352 is missing expected H atoms. Skipping.
Residue THR  546 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  597 is missing expected H atoms. Skipping.
Residue TYR  608 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  750 is missing expected H atoms. Skipping.
Residue MET  816 is missing expected H atoms. Skipping.
Residue LYS  894 is missing expected H atoms. Skipping.
Residue MET  931 is missing expected H atoms. Skipping.
Evaluate side-chains
  178 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 175
  time to evaluate  : 1.866 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  504 GLU cc_start: 0.8216 (mt-10) cc_final: 0.8009 (mt-10)
REVERT: B  371 GLU cc_start: 0.8745 (tt0) cc_final: 0.8251 (tp30)
REVERT: B  499 LYS cc_start: 0.8990 (mptt) cc_final: 0.8716 (mptt)
REVERT: B  520 LYS cc_start: 0.8605 (mmmt) cc_final: 0.8177 (mmmm)
REVERT: B  676 LEU cc_start: 0.8592 (mt) cc_final: 0.8388 (mt)
REVERT: B  677 MET cc_start: 0.8782 (tpt) cc_final: 0.8489 (tmm)
REVERT: B  734 LEU cc_start: 0.9128 (mm) cc_final: 0.8883 (mm)
REVERT: B  807 TYR cc_start: 0.7842 (t80) cc_final: 0.7599 (t80)
REVERT: B  886 MET cc_start: 0.8584 (mtm) cc_final: 0.8292 (mtm)
  outliers start: 3
  outliers final: 2
  residues processed: 178
  average time/residue: 0.4698
  time to fit residues: 125.5777
Evaluate side-chains
  144 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 142
  time to evaluate  : 1.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 135 optimal weight:    8.9990
   chunk 39 optimal weight:    5.9990
   chunk 47 optimal weight:    9.9990
   chunk 64 optimal weight:    4.9990
   chunk 41 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 125 optimal weight:    9.9990
   chunk 70 optimal weight:    9.9990
   chunk 9 optimal weight:    0.7980
   chunk 137 optimal weight:    9.9990
   overall best weight:    6.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 ASN
B 678 ASN
** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.088026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.065243 restraints weight = 120001.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.068644 restraints weight = 50689.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.070773 restraints weight = 31209.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.4912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072  12278  Z= 0.287
  Angle     :  0.680   7.513  16816  Z= 0.369
  Chirality :  0.042   0.180   1954
  Planarity :  0.004   0.062   1924
  Dihedral  : 15.044  81.099   2374
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.22), residues: 1330
  helix:  0.74 (0.19), residues: 714
  sheet: -2.35 (0.34), residues: 168
  loop : -2.96 (0.24), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 737 
 HIS   0.011   0.002   HIS A 927 
 PHE   0.018   0.002   PHE A 680 
 TYR   0.017   0.002   TYR B 408 
 ARG   0.009   0.001   ARG A 728 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04968 (  656)
  hydrogen bonds       : angle       4.83904 ( 1818)
  metal coordination   : bond        0.01351 (    8)
  metal coordination   : angle       2.31885 (   12)
  covalent geometry    : bond        0.00587 (12270)
  covalent geometry    : angle       0.67737 (16804)

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  352 is missing expected H atoms. Skipping.
Residue THR  546 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  597 is missing expected H atoms. Skipping.
Residue TYR  608 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  750 is missing expected H atoms. Skipping.
Residue MET  816 is missing expected H atoms. Skipping.
Residue LYS  894 is missing expected H atoms. Skipping.
Residue MET  931 is missing expected H atoms. Skipping.
Residue LYS  352 is missing expected H atoms. Skipping.
Residue THR  546 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  597 is missing expected H atoms. Skipping.
Residue TYR  608 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  750 is missing expected H atoms. Skipping.
Residue MET  816 is missing expected H atoms. Skipping.
Residue LYS  894 is missing expected H atoms. Skipping.
Residue MET  931 is missing expected H atoms. Skipping.
Evaluate side-chains
  177 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 1.971 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  926 MET cc_start: 0.8488 (ptp) cc_final: 0.8285 (ptp)
REVERT: B  371 GLU cc_start: 0.8735 (tt0) cc_final: 0.8258 (tp30)
REVERT: B  499 LYS cc_start: 0.9141 (mptt) cc_final: 0.8786 (mptt)
REVERT: B  520 LYS cc_start: 0.8564 (mmmt) cc_final: 0.8160 (mmmm)
REVERT: B  677 MET cc_start: 0.8729 (tpt) cc_final: 0.8499 (tmm)
REVERT: B  807 TYR cc_start: 0.7857 (t80) cc_final: 0.7628 (t80)
REVERT: B  886 MET cc_start: 0.8637 (mtm) cc_final: 0.8337 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.4871
  time to fit residues: 129.6230
Evaluate side-chains
  139 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 1.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 27 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 31 optimal weight:   10.0000
   chunk 100 optimal weight:   10.0000
   chunk 119 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 87 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 99 optimal weight:    6.9990
   chunk 113 optimal weight:    9.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 313 GLN
** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 862 GLN
B 919 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.090879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.068181 restraints weight = 116114.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.071704 restraints weight = 50303.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.073927 restraints weight = 30857.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.4996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12278  Z= 0.125
  Angle     :  0.530   5.606  16816  Z= 0.286
  Chirality :  0.039   0.177   1954
  Planarity :  0.003   0.033   1924
  Dihedral  : 14.737  83.494   2374
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.22), residues: 1330
  helix:  1.30 (0.19), residues: 714
  sheet: -1.86 (0.35), residues: 180
  loop : -2.72 (0.26), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B1003 
 HIS   0.004   0.001   HIS A 626 
 PHE   0.015   0.001   PHE A 680 
 TYR   0.027   0.001   TYR A 624 
 ARG   0.004   0.000   ARG A 890 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04067 (  656)
  hydrogen bonds       : angle       4.34994 ( 1818)
  metal coordination   : bond        0.00478 (    8)
  metal coordination   : angle       1.44174 (   12)
  covalent geometry    : bond        0.00255 (12270)
  covalent geometry    : angle       0.52865 (16804)

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  352 is missing expected H atoms. Skipping.
Residue THR  546 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  597 is missing expected H atoms. Skipping.
Residue TYR  608 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  750 is missing expected H atoms. Skipping.
Residue MET  816 is missing expected H atoms. Skipping.
Residue LYS  894 is missing expected H atoms. Skipping.
Residue MET  931 is missing expected H atoms. Skipping.
Residue LYS  352 is missing expected H atoms. Skipping.
Residue THR  546 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  597 is missing expected H atoms. Skipping.
Residue TYR  608 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  750 is missing expected H atoms. Skipping.
Residue MET  816 is missing expected H atoms. Skipping.
Residue LYS  894 is missing expected H atoms. Skipping.
Residue MET  931 is missing expected H atoms. Skipping.
Evaluate side-chains
  180 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 1.803 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  676 LEU cc_start: 0.8584 (mt) cc_final: 0.8275 (mt)
REVERT: A  882 LEU cc_start: 0.9288 (tp) cc_final: 0.9061 (tp)
REVERT: A  926 MET cc_start: 0.8318 (ptp) cc_final: 0.8024 (ptp)
REVERT: B  371 GLU cc_start: 0.8698 (tt0) cc_final: 0.8195 (tp30)
REVERT: B  499 LYS cc_start: 0.9067 (mptt) cc_final: 0.8745 (mptt)
REVERT: B  520 LYS cc_start: 0.8509 (mmmt) cc_final: 0.8182 (mmmm)
REVERT: B  807 TYR cc_start: 0.7700 (t80) cc_final: 0.7459 (t80)
REVERT: B  886 MET cc_start: 0.8625 (mtm) cc_final: 0.8405 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 180
  average time/residue: 0.4647
  time to fit residues: 126.5097
Evaluate side-chains
  143 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 1.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 95 optimal weight:    2.9990
   chunk 131 optimal weight:   10.0000
   chunk 123 optimal weight:    9.9990
   chunk 60 optimal weight:   10.0000
   chunk 114 optimal weight:    8.9990
   chunk 14 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 78 optimal weight:    6.9990
   chunk 106 optimal weight:    4.9990
   chunk 133 optimal weight:    0.9980
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 919 ASN ** 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 = 0.3732 r_free = 0.3732 target = 0.090824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.068229 restraints weight = 113569.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.071771 restraints weight = 47856.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.073997 restraints weight = 28920.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.5123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12278  Z= 0.136
  Angle     :  0.529   5.145  16816  Z= 0.288
  Chirality :  0.038   0.174   1954
  Planarity :  0.003   0.034   1924
  Dihedral  : 14.623  80.435   2374
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  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: -0.48 (0.23), residues: 1330
  helix:  1.44 (0.19), residues: 714
  sheet: -1.89 (0.35), residues: 180
  loop : -2.66 (0.26), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 582 
 HIS   0.005   0.001   HIS B 974 
 PHE   0.018   0.001   PHE A 680 
 TYR   0.022   0.001   TYR A 565 
 ARG   0.004   0.000   ARG A 890 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04078 (  656)
  hydrogen bonds       : angle       4.29727 ( 1818)
  metal coordination   : bond        0.00518 (    8)
  metal coordination   : angle       1.27735 (   12)
  covalent geometry    : bond        0.00282 (12270)
  covalent geometry    : angle       0.52769 (16804)

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  352 is missing expected H atoms. Skipping.
Residue THR  546 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  597 is missing expected H atoms. Skipping.
Residue TYR  608 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  750 is missing expected H atoms. Skipping.
Residue MET  816 is missing expected H atoms. Skipping.
Residue LYS  894 is missing expected H atoms. Skipping.
Residue MET  931 is missing expected H atoms. Skipping.
Residue LYS  352 is missing expected H atoms. Skipping.
Residue THR  546 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  597 is missing expected H atoms. Skipping.
Residue TYR  608 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  750 is missing expected H atoms. Skipping.
Residue MET  816 is missing expected H atoms. Skipping.
Residue LYS  894 is missing expected H atoms. Skipping.
Residue MET  931 is missing expected H atoms. Skipping.
Evaluate side-chains
  176 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 2.071 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  470 ASN cc_start: 0.7379 (m110) cc_final: 0.7165 (m110)
REVERT: A  847 ASN cc_start: 0.8410 (m-40) cc_final: 0.8203 (m-40)
REVERT: A  882 LEU cc_start: 0.9362 (tp) cc_final: 0.9041 (tp)
REVERT: A  926 MET cc_start: 0.8379 (ptp) cc_final: 0.8067 (ptp)
REVERT: B  371 GLU cc_start: 0.8740 (tt0) cc_final: 0.8198 (tp30)
REVERT: B  394 ASP cc_start: 0.8349 (p0) cc_final: 0.7772 (t0)
REVERT: B  499 LYS cc_start: 0.9134 (mptt) cc_final: 0.8798 (mptt)
REVERT: B  520 LYS cc_start: 0.8507 (mmmt) cc_final: 0.8174 (mmmm)
REVERT: B  886 MET cc_start: 0.8669 (mtm) cc_final: 0.8446 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.4362
  time to fit residues: 118.8769
Evaluate side-chains
  148 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 1.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 119 optimal weight:   20.0000
   chunk 89 optimal weight:    5.9990
   chunk 118 optimal weight:   20.0000
   chunk 115 optimal weight:    7.9990
   chunk 102 optimal weight:   10.0000
   chunk 123 optimal weight:    7.9990
   chunk 3 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 35 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 30 optimal weight:    4.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 986 ASN
** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 919 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 = 0.3683 r_free = 0.3683 target = 0.088408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.066148 restraints weight = 116358.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.069540 restraints weight = 50031.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.071629 restraints weight = 30584.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.5616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  12278  Z= 0.258
  Angle     :  0.630   6.502  16816  Z= 0.346
  Chirality :  0.041   0.154   1954
  Planarity :  0.004   0.040   1924
  Dihedral  : 14.970  83.659   2374
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.12 %
    Favored  : 91.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  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: -1.05 (0.22), residues: 1330
  helix:  1.09 (0.19), residues: 698
  sheet: -2.28 (0.34), residues: 184
  loop : -2.93 (0.24), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 968 
 HIS   0.005   0.002   HIS A 927 
 PHE   0.021   0.002   PHE A 680 
 TYR   0.016   0.002   TYR B 408 
 ARG   0.008   0.001   ARG A 890 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04897 (  656)
  hydrogen bonds       : angle       4.65149 ( 1818)
  metal coordination   : bond        0.01197 (    8)
  metal coordination   : angle       1.84613 (   12)
  covalent geometry    : bond        0.00525 (12270)
  covalent geometry    : angle       0.62864 (16804)

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  352 is missing expected H atoms. Skipping.
Residue THR  546 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  597 is missing expected H atoms. Skipping.
Residue TYR  608 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  750 is missing expected H atoms. Skipping.
Residue MET  816 is missing expected H atoms. Skipping.
Residue LYS  894 is missing expected H atoms. Skipping.
Residue MET  931 is missing expected H atoms. Skipping.
Residue LYS  352 is missing expected H atoms. Skipping.
Residue THR  546 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  597 is missing expected H atoms. Skipping.
Residue TYR  608 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  750 is missing expected H atoms. Skipping.
Residue MET  816 is missing expected H atoms. Skipping.
Residue LYS  894 is missing expected H atoms. Skipping.
Residue MET  931 is missing expected H atoms. Skipping.
Evaluate side-chains
  171 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 2.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  926 MET cc_start: 0.8452 (ptp) cc_final: 0.8156 (ptp)
REVERT: B  371 GLU cc_start: 0.8693 (tt0) cc_final: 0.8213 (tp30)
REVERT: B  465 GLN cc_start: 0.8638 (tp40) cc_final: 0.7930 (tp40)
REVERT: B  499 LYS cc_start: 0.9157 (mptt) cc_final: 0.8848 (mptt)
REVERT: B  520 LYS cc_start: 0.8505 (mmmt) cc_final: 0.8142 (mmmm)
REVERT: B  886 MET cc_start: 0.8683 (mtm) cc_final: 0.8459 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.6576
  time to fit residues: 169.2770
Evaluate side-chains
  140 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 3.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 68 optimal weight:    7.9990
   chunk 59 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 101 optimal weight:    6.9990
   chunk 25 optimal weight:   10.0000
   chunk 46 optimal weight:    9.9990
   chunk 54 optimal weight:    6.9990
   chunk 109 optimal weight:   10.0000
   chunk 36 optimal weight:    9.9990
   chunk 55 optimal weight:    6.9990
   chunk 107 optimal weight:    5.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 928 HIS
** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 919 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 = 0.3688 r_free = 0.3688 target = 0.088382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.066019 restraints weight = 117455.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.069536 restraints weight = 49164.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.071693 restraints weight = 29901.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.5921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  12278  Z= 0.224
  Angle     :  0.599   6.409  16816  Z= 0.327
  Chirality :  0.040   0.152   1954
  Planarity :  0.004   0.037   1924
  Dihedral  : 14.958  89.934   2374
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.12 %
    Favored  : 91.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  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 (0.22), residues: 1330
  helix:  1.14 (0.19), residues: 696
  sheet: -2.50 (0.33), residues: 196
  loop : -3.00 (0.24), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 582 
 HIS   0.008   0.001   HIS B 974 
 PHE   0.019   0.002   PHE A 680 
 TYR   0.014   0.002   TYR B 408 
 ARG   0.005   0.001   ARG A 468 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04537 (  656)
  hydrogen bonds       : angle       4.58887 ( 1818)
  metal coordination   : bond        0.00988 (    8)
  metal coordination   : angle       1.53429 (   12)
  covalent geometry    : bond        0.00453 (12270)
  covalent geometry    : angle       0.59751 (16804)

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  352 is missing expected H atoms. Skipping.
Residue THR  546 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  597 is missing expected H atoms. Skipping.
Residue TYR  608 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  750 is missing expected H atoms. Skipping.
Residue MET  816 is missing expected H atoms. Skipping.
Residue LYS  894 is missing expected H atoms. Skipping.
Residue MET  931 is missing expected H atoms. Skipping.
Residue LYS  352 is missing expected H atoms. Skipping.
Residue THR  546 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  597 is missing expected H atoms. Skipping.
Residue TYR  608 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  750 is missing expected H atoms. Skipping.
Residue MET  816 is missing expected H atoms. Skipping.
Residue LYS  894 is missing expected H atoms. Skipping.
Residue MET  931 is missing expected H atoms. Skipping.
Evaluate side-chains
  164 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 1.987 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  847 ASN cc_start: 0.8259 (m-40) cc_final: 0.8028 (m-40)
REVERT: A  882 LEU cc_start: 0.9397 (tp) cc_final: 0.9067 (tp)
REVERT: A  926 MET cc_start: 0.8477 (ptp) cc_final: 0.8160 (ptp)
REVERT: B  465 GLN cc_start: 0.8647 (tp40) cc_final: 0.7908 (tp40)
REVERT: B  499 LYS cc_start: 0.9119 (mptt) cc_final: 0.8855 (mptt)
REVERT: B  520 LYS cc_start: 0.8529 (mmmt) cc_final: 0.8119 (mmmm)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.5612
  time to fit residues: 141.4704
Evaluate side-chains
  138 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 2.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 39 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 49 optimal weight:   10.0000
   chunk 27 optimal weight:    0.9980
   chunk 29 optimal weight:    6.9990
   chunk 111 optimal weight:    8.9990
   chunk 66 optimal weight:    0.0040
   chunk 72 optimal weight:    2.9990
   chunk 130 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.9998

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

Flipped N/Q/H residues before XYZ refinement:
** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 919 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.089955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.067413 restraints weight = 116983.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.071016 restraints weight = 49269.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.073281 restraints weight = 29995.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.5965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12278  Z= 0.134
  Angle     :  0.543   6.278  16816  Z= 0.295
  Chirality :  0.039   0.149   1954
  Planarity :  0.003   0.035   1924
  Dihedral  : 14.730  89.123   2374
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  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: -0.71 (0.23), residues: 1330
  helix:  1.45 (0.19), residues: 698
  sheet: -2.28 (0.33), residues: 196
  loop : -2.85 (0.25), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1003 
 HIS   0.005   0.001   HIS A 604 
 PHE   0.018   0.001   PHE A 849 
 TYR   0.013   0.001   TYR A 624 
 ARG   0.007   0.000   ARG A 890 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04090 (  656)
  hydrogen bonds       : angle       4.33319 ( 1818)
  metal coordination   : bond        0.00494 (    8)
  metal coordination   : angle       1.36970 (   12)
  covalent geometry    : bond        0.00281 (12270)
  covalent geometry    : angle       0.54227 (16804)

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  352 is missing expected H atoms. Skipping.
Residue THR  546 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  597 is missing expected H atoms. Skipping.
Residue TYR  608 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  750 is missing expected H atoms. Skipping.
Residue MET  816 is missing expected H atoms. Skipping.
Residue LYS  894 is missing expected H atoms. Skipping.
Residue MET  931 is missing expected H atoms. Skipping.
Residue LYS  352 is missing expected H atoms. Skipping.
Residue THR  546 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  597 is missing expected H atoms. Skipping.
Residue TYR  608 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  750 is missing expected H atoms. Skipping.
Residue MET  816 is missing expected H atoms. Skipping.
Residue LYS  894 is missing expected H atoms. Skipping.
Residue MET  931 is missing expected H atoms. Skipping.
Evaluate side-chains
  173 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 2.607 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  462 TYR cc_start: 0.8904 (t80) cc_final: 0.8629 (t80)
REVERT: A  882 LEU cc_start: 0.9222 (tp) cc_final: 0.8977 (tt)
REVERT: A  926 MET cc_start: 0.8327 (ptp) cc_final: 0.7972 (ptp)
REVERT: B  371 GLU cc_start: 0.8723 (tt0) cc_final: 0.8179 (tp30)
REVERT: B  394 ASP cc_start: 0.8416 (p0) cc_final: 0.7848 (t0)
REVERT: B  399 ILE cc_start: 0.7654 (mt) cc_final: 0.7453 (mp)
REVERT: B  499 LYS cc_start: 0.9106 (mptt) cc_final: 0.8835 (mptt)
REVERT: B  520 LYS cc_start: 0.8522 (mmmt) cc_final: 0.8171 (mmmm)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.5464
  time to fit residues: 147.7760
Evaluate side-chains
  151 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 3.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 76 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 102 optimal weight:    7.9990
   chunk 34 optimal weight:    0.0370
   chunk 70 optimal weight:    5.9990
   chunk 35 optimal weight:    0.8980
   chunk 110 optimal weight:   10.0000
   chunk 54 optimal weight:    9.9990
   chunk 15 optimal weight:    3.9990
   chunk 99 optimal weight:   10.0000
   overall best weight:    1.3462

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

Flipped N/Q/H residues before XYZ refinement:
** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 416 GLN
B 475 GLN
** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 919 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.090708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.068447 restraints weight = 116406.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.072119 restraints weight = 48544.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.074444 restraints weight = 29057.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.5984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  12278  Z= 0.116
  Angle     :  0.521   6.234  16816  Z= 0.282
  Chirality :  0.038   0.141   1954
  Planarity :  0.003   0.034   1924
  Dihedral  : 14.536  87.765   2374
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  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: -0.44 (0.23), residues: 1330
  helix:  1.64 (0.19), residues: 698
  sheet: -1.99 (0.34), residues: 192
  loop : -2.76 (0.25), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 582 
 HIS   0.004   0.001   HIS B 974 
 PHE   0.015   0.001   PHE A 680 
 TYR   0.015   0.001   TYR A 624 
 ARG   0.004   0.000   ARG A 599 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03853 (  656)
  hydrogen bonds       : angle       4.19481 ( 1818)
  metal coordination   : bond        0.00346 (    8)
  metal coordination   : angle       1.38633 (   12)
  covalent geometry    : bond        0.00247 (12270)
  covalent geometry    : angle       0.51989 (16804)

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  352 is missing expected H atoms. Skipping.
Residue THR  546 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  597 is missing expected H atoms. Skipping.
Residue TYR  608 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  750 is missing expected H atoms. Skipping.
Residue MET  816 is missing expected H atoms. Skipping.
Residue LYS  894 is missing expected H atoms. Skipping.
Residue MET  931 is missing expected H atoms. Skipping.
Residue LYS  352 is missing expected H atoms. Skipping.
Residue THR  546 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  597 is missing expected H atoms. Skipping.
Residue TYR  608 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  750 is missing expected H atoms. Skipping.
Residue MET  816 is missing expected H atoms. Skipping.
Residue LYS  894 is missing expected H atoms. Skipping.
Residue MET  931 is missing expected H atoms. Skipping.
Evaluate side-chains
  172 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 1.927 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  462 TYR cc_start: 0.8868 (t80) cc_final: 0.8537 (t80)
REVERT: A  882 LEU cc_start: 0.9271 (tp) cc_final: 0.8985 (tt)
REVERT: A  926 MET cc_start: 0.8309 (ptp) cc_final: 0.8068 (ptp)
REVERT: B  394 ASP cc_start: 0.8249 (p0) cc_final: 0.7769 (t0)
REVERT: B  499 LYS cc_start: 0.9104 (mptt) cc_final: 0.8844 (mptt)
REVERT: B  520 LYS cc_start: 0.8505 (mmmt) cc_final: 0.8294 (mmmm)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.4541
  time to fit residues: 118.2592
Evaluate side-chains
  149 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 1.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 84 optimal weight:   10.0000
   chunk 11 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 26 optimal weight:   10.0000
   chunk 43 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 109 optimal weight:   10.0000
   chunk 46 optimal weight:    9.9990
   chunk 10 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 919 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.090850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.068772 restraints weight = 115646.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.072396 restraints weight = 48981.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.074658 restraints weight = 29518.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.6029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12278  Z= 0.119
  Angle     :  0.525   6.203  16816  Z= 0.283
  Chirality :  0.038   0.194   1954
  Planarity :  0.003   0.033   1924
  Dihedral  : 14.482  86.656   2374
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.23), residues: 1330
  helix:  1.82 (0.19), residues: 686
  sheet: -1.97 (0.34), residues: 192
  loop : -2.54 (0.26), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 582 
 HIS   0.006   0.001   HIS B 927 
 PHE   0.016   0.001   PHE A 680 
 TYR   0.013   0.001   TYR A 624 
 ARG   0.004   0.000   ARG B 822 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03913 (  656)
  hydrogen bonds       : angle       4.16524 ( 1818)
  metal coordination   : bond        0.00314 (    8)
  metal coordination   : angle       1.28657 (   12)
  covalent geometry    : bond        0.00253 (12270)
  covalent geometry    : angle       0.52444 (16804)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7503.26 seconds
wall clock time: 133 minutes 18.14 seconds (7998.14 seconds total)