Starting phenix.real_space_refine
on Thu Jul 24 22:49:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8afe_15395/07_2025/8afe_15395.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8afe_15395/07_2025/8afe_15395.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8afe_15395/07_2025/8afe_15395.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8afe_15395/07_2025/8afe_15395.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8afe_15395/07_2025/8afe_15395.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8afe_15395/07_2025/8afe_15395.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      23      5.16       5
     C    4124      2.51       5
     N    1282      2.21       5
     O    1356      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6785
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 739
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 739
          Classifications: {'peptide': 96}
          Link IDs: {'TRANS': 95}
    Chain: "B"
      Number of atoms: 747
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 747
          Classifications: {'peptide': 97}
          Link IDs: {'TRANS': 96}
    Chain: "D"
      Number of atoms: 869
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 869
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 2, 'TRANS': 109}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 869
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 869
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 2, 'TRANS': 109}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 600
          Classifications: {'peptide': 79}
          Link IDs: {'TRANS': 78}
    Chain: "F"
      Number of atoms: 600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 600
          Classifications: {'peptide': 79}
          Link IDs: {'TRANS': 78}
    Chain: "G"
      Number of atoms: 333
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 333
          Classifications: {'peptide': 43}
          Link IDs: {'TRANS': 42}
    Chain: "H"
      Number of atoms: 299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 299
          Classifications: {'peptide': 39}
          Link IDs: {'TRANS': 38}
    Chain: "I"
      Number of atoms: 860
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 860
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 2, 'TRANS': 108}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 869
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 869
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 2, 'TRANS': 109}
          Chain breaks: 1
  Time building chain proxies: 5.25, per 1000 atoms: 0.77
  Number of scatterers: 6785
  At special positions: 0
  Unit cell: (63.6, 242.475, 88.775, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      23     16.00
     O    1356      8.00
     N    1282      7.00
     C    4124      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 795 " - pdb=" SG  CYS D 868 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 795 " - pdb=" SG  CYS C 868 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 795 " - pdb=" SG  CYS I 868 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J 795 " - pdb=" SG  CYS J 868 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.80
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1648

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 13 sheets defined
      50.3% alpha, 19.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 350 through 357
      removed outlier: 3.961A  pdb=" N   ASP A 354 " --> pdb=" O   HIS A 350 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   THR A 355 " --> pdb=" O   ALA A 351 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ARG A 357 " --> pdb=" O   VAL A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 441
      removed outlier: 3.647A  pdb=" N   GLU A 362 " --> pdb=" O   ALA A 358 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   ARG A 363 " --> pdb=" O   THR A 359 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA A 364 " --> pdb=" O   ALA A 360 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ALA A 368 " --> pdb=" O   ALA A 364 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LYS A 369 " --> pdb=" O   ASP A 365 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   VAL A 372 " --> pdb=" O   ALA A 368 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   SER A 425 " --> pdb=" O   GLU A 421 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   GLU A 426 " --> pdb=" O   ARG A 422 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ARG A 441 " --> pdb=" O   ALA A 437 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 352 through 432
      removed outlier: 3.877A  pdb=" N   ALA B 356 " --> pdb=" O   GLY B 352 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLU B 362 " --> pdb=" O   ALA B 358 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LEU B 367 " --> pdb=" O   ARG B 363 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ALA B 371 " --> pdb=" O   LEU B 367 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   VAL B 372 " --> pdb=" O   ALA B 368 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   GLU B 383 " --> pdb=" O   LYS B 379 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ARG B 404 " --> pdb=" O   ASP B 400 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ILE B 420 " --> pdb=" O   LEU B 416 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LEU B 429 " --> pdb=" O   SER B 425 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 442
    Processing helix  chain 'B' and resid 443 through 446
    Processing helix  chain 'D' and resid 859 through 863
      removed outlier: 3.554A  pdb=" N   THR D 863 " --> pdb=" O   PRO D 860 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 859 through 863
      removed outlier: 3.892A  pdb=" N   THR C 863 " --> pdb=" O   PRO C 860 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 86 through 163
      removed outlier: 3.828A  pdb=" N   LEU E 115 " --> pdb=" O   VAL E 111 " (cutoff:3.500A)
      removed outlier: 4.883A  pdb=" N   ALA E 116 " --> pdb=" O   SER E 112 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 86 through 163
      removed outlier: 3.591A  pdb=" N   ALA F  92 " --> pdb=" O   ILE F  88 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   ASN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 404 through 439
      removed outlier: 3.796A  pdb=" N   ALA G 411 " --> pdb=" O   ALA G 407 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LYS G 412 " --> pdb=" O   THR G 408 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ALA G 418 " --> pdb=" O   ALA G 414 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   GLU G 426 " --> pdb=" O   ARG G 422 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   ALA G 427 " --> pdb=" O   LEU G 423 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LEU G 429 " --> pdb=" O   SER G 425 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ALA G 433 " --> pdb=" O   LEU G 429 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 440 through 444
    Processing helix  chain 'H' and resid 405 through 431
      removed outlier: 3.648A  pdb=" N   HIS H 409 " --> pdb=" O   ASP H 405 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   GLU H 410 " --> pdb=" O   SER H 406 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ILE H 420 " --> pdb=" O   LEU H 416 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLU H 421 " --> pdb=" O   GLN H 417 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 432 through 441
      removed outlier: 3.589A  pdb=" N   ASP H 440 " --> pdb=" O   ALA H 436 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ARG H 441 " --> pdb=" O   ALA H 437 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 859 through 863
      removed outlier: 3.602A  pdb=" N   THR I 863 " --> pdb=" O   PRO I 860 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 859 through 863
      removed outlier: 3.819A  pdb=" N   THR J 863 " --> pdb=" O   PRO J 860 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 6 through 7
      removed outlier: 3.711A  pdb=" N   VAL D 851 " --> pdb=" O   CYS D 795 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   THR D 850 " --> pdb=" O   ASP D 845 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 12
      removed outlier: 6.212A  pdb=" N   GLY D  10 " --> pdb=" O   THR D 885 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   MET D 807 " --> pdb=" O   VAL D 823 " (cutoff:3.500A)
      removed outlier: 5.115A  pdb=" N   VAL D 823 " --> pdb=" O   MET D 807 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   TRP D 809 " --> pdb=" O   VAL D 821 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 870 through 872
    Processing sheet with id=AA4, first strand: chain 'C' and resid 5 through 7
    Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.550A  pdb=" N   VAL C  12 " --> pdb=" O   THR C 885 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 830 through 832
      removed outlier: 7.030A  pdb=" N   TRP C 809 " --> pdb=" O   VAL C 821 " (cutoff:3.500A)
      removed outlier: 5.109A  pdb=" N   VAL C 823 " --> pdb=" O   MET C 807 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   MET C 807 " --> pdb=" O   VAL C 823 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'I' and resid 5 through 6
      removed outlier: 3.613A  pdb=" N   VAL I 851 " --> pdb=" O   CYS I 795 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'I' and resid 10 through 12
      removed outlier: 6.809A  pdb=" N   MET I 807 " --> pdb=" O   VAL I 823 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   VAL I 823 " --> pdb=" O   MET I 807 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   TRP I 809 " --> pdb=" O   VAL I 821 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'I' and resid 870 through 872
      removed outlier: 3.571A  pdb=" N   TYR I 872 " --> pdb=" O   SER I 875 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'J' and resid 4 through 6
    Processing sheet with id=AB2, first strand: chain 'J' and resid 10 through 12
      removed outlier: 6.544A  pdb=" N   GLY J  10 " --> pdb=" O   THR J 885 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'J' and resid 10 through 12
      removed outlier: 6.544A  pdb=" N   GLY J  10 " --> pdb=" O   THR J 885 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'J' and resid 792 through 793

    463 hydrogen bonds defined for protein.
    1293 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.12

  Time building geometry restraints manager: 2.15 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2430
        1.34 -     1.46: 1083
        1.46 -     1.58: 3290
        1.58 -     1.70: 0
        1.70 -     1.81: 38
  Bond restraints: 6841
  Sorted by residual:
  bond pdb=" CB  TRP C 827 "
       pdb=" CG  TRP C 827 "
    ideal  model  delta    sigma   weight residual
    1.498  1.446  0.052 3.10e-02 1.04e+03 2.78e+00
  bond pdb=" CG1 ILE D 806 "
       pdb=" CD1 ILE D 806 "
    ideal  model  delta    sigma   weight residual
    1.513  1.463  0.050 3.90e-02 6.57e+02 1.67e+00
  bond pdb=" C   TYR J 832 "
       pdb=" N   VAL J 833 "
    ideal  model  delta    sigma   weight residual
    1.334  1.317  0.016 1.29e-02 6.01e+03 1.62e+00
  bond pdb=" CB  ASN I 869 "
       pdb=" CG  ASN I 869 "
    ideal  model  delta    sigma   weight residual
    1.516  1.484  0.032 2.50e-02 1.60e+03 1.59e+00
  bond pdb=" C   LYS D 859 "
       pdb=" N   PRO D 860 "
    ideal  model  delta    sigma   weight residual
    1.337  1.323  0.014 1.11e-02 8.12e+03 1.49e+00
  ... (remaining 6836 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.17: 8401
        1.17 -     2.34: 683
        2.34 -     3.51: 99
        3.51 -     4.68: 19
        4.68 -     5.85: 7
  Bond angle restraints: 9209
  Sorted by residual:
  angle pdb=" N   ILE J 806 "
        pdb=" CA  ILE J 806 "
        pdb=" C   ILE J 806 "
      ideal   model   delta    sigma   weight residual
     108.93  113.36   -4.43 1.35e+00 5.49e-01 1.08e+01
  angle pdb=" N   ILE D 806 "
        pdb=" CA  ILE D 806 "
        pdb=" C   ILE D 806 "
      ideal   model   delta    sigma   weight residual
     109.30  113.38   -4.08 1.31e+00 5.83e-01 9.70e+00
  angle pdb=" C   ALA E 118 "
        pdb=" N   GLU E 119 "
        pdb=" CA  GLU E 119 "
      ideal   model   delta    sigma   weight residual
     120.68  115.81    4.87 1.70e+00 3.46e-01 8.22e+00
  angle pdb=" C   SER E 112 "
        pdb=" N   ALA E 113 "
        pdb=" CA  ALA E 113 "
      ideal   model   delta    sigma   weight residual
     122.42  118.24    4.18 1.55e+00 4.16e-01 7.29e+00
  angle pdb=" CA  TRP C 827 "
        pdb=" CB  TRP C 827 "
        pdb=" CG  TRP C 827 "
      ideal   model   delta    sigma   weight residual
     113.60  108.52    5.08 1.90e+00 2.77e-01 7.16e+00
  ... (remaining 9204 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.25: 3786
       17.25 -    34.51: 381
       34.51 -    51.76: 46
       51.76 -    69.02: 6
       69.02 -    86.27: 14
  Dihedral angle restraints: 4233
    sinusoidal: 1691
      harmonic: 2542
  Sorted by residual:
  dihedral pdb=" CB  CYS C 795 "
           pdb=" SG  CYS C 795 "
           pdb=" SG  CYS C 868 "
           pdb=" CB  CYS C 868 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   43.73   49.27     1      1.00e+01 1.00e-02 3.34e+01
  dihedral pdb=" CB  CYS I 795 "
           pdb=" SG  CYS I 795 "
           pdb=" SG  CYS I 868 "
           pdb=" CB  CYS I 868 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   44.90   48.10     1      1.00e+01 1.00e-02 3.19e+01
  dihedral pdb=" CA  HIS A 350 "
           pdb=" C   HIS A 350 "
           pdb=" N   ALA A 351 "
           pdb=" CA  ALA A 351 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.67  -25.33     0      5.00e+00 4.00e-02 2.57e+01
  ... (remaining 4230 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 711
       0.039 -    0.079: 242
       0.079 -    0.118: 79
       0.118 -    0.158: 4
       0.158 -    0.197: 5
  Chirality restraints: 1041
  Sorted by residual:
  chirality pdb=" CB  ILE J 842 "
            pdb=" CA  ILE J 842 "
            pdb=" CG1 ILE J 842 "
            pdb=" CG2 ILE J 842 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.72e-01
  chirality pdb=" CB  ILE I 842 "
            pdb=" CA  ILE I 842 "
            pdb=" CG1 ILE I 842 "
            pdb=" CG2 ILE I 842 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.14e-01
  chirality pdb=" CB  VAL J 823 "
            pdb=" CA  VAL J 823 "
            pdb=" CG1 VAL J 823 "
            pdb=" CG2 VAL J 823 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.18 2.00e-01 2.50e+01 8.50e-01
  ... (remaining 1038 not shown)

  Planarity restraints: 1219
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 859 "    0.057 5.00e-02 4.00e+02   8.65e-02 1.20e+01
        pdb=" N   PRO C 860 "   -0.150 5.00e-02 4.00e+02
        pdb=" CA  PRO C 860 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO C 860 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B 417 "   -0.011 2.00e-02 2.50e+03   2.26e-02 5.12e+00
        pdb=" CD  GLN B 417 "    0.039 2.00e-02 2.50e+03
        pdb=" OE1 GLN B 417 "   -0.015 2.00e-02 2.50e+03
        pdb=" NE2 GLN B 417 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS J 859 "    0.024 5.00e-02 4.00e+02   3.70e-02 2.19e+00
        pdb=" N   PRO J 860 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO J 860 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO J 860 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1216 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 272
        2.71 -     3.26: 6877
        3.26 -     3.80: 10416
        3.80 -     4.35: 13277
        4.35 -     4.90: 22214
  Nonbonded interactions: 53056
  Sorted by model distance:
  nonbonded pdb=" O   THR B 424 "
            pdb=" ND2 ASN C 831 "
     model   vdw
     2.161 3.120
  nonbonded pdb=" NH1 ARG D 799 "
            pdb=" OG  SER D 800 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" OD1 ASP I 802 "
            pdb=" NH2 ARG I 844 "
     model   vdw
     2.245 3.120
  nonbonded pdb=" NH1 ARG I 808 "
            pdb=" OH  TYR I 810 "
     model   vdw
     2.245 3.120
  nonbonded pdb=" O   ASP C 862 "
            pdb=" OH  TYR C 866 "
     model   vdw
     2.255 3.040
  ... (remaining 53051 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and resid 350 through 445)
}
ncs_group {
  reference = (chain 'C' and resid 2 through 887)
  selection = (chain 'D' and resid 2 through 887)
  selection = chain 'I'
  selection = (chain 'J' and resid 2 through 887)
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'G' and resid 403 through 441)
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.660
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6057
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      :  0.006   0.052   6845  Z= 0.272
  Angle     :  0.700   5.850   9217  Z= 0.430
  Chirality :  0.044   0.197   1041
  Planarity :  0.004   0.086   1219
  Dihedral  : 14.166  86.270   2573
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  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: -1.30 (0.28), residues: 852
  helix: -0.24 (0.25), residues: 379
  sheet: -2.06 (0.31), residues: 239
  loop :  0.03 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP C 827 
 HIS   0.005   0.002   HIS A 350 
 PHE   0.005   0.001   PHE I 840 
 TYR   0.018   0.002   TYR J  13 
 ARG   0.013   0.001   ARG B 404 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21907 (  459)
  hydrogen bonds       : angle       9.24475 ( 1293)
  SS BOND              : bond        0.00226 (    4)
  SS BOND              : angle       1.61102 (    8)
  covalent geometry    : bond        0.00580 ( 6841)
  covalent geometry    : angle       0.69894 ( 9209)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
REVERT: C  865 VAL cc_start: 0.7852 (m) cc_final: 0.7637 (p)
REVERT: I  862 ASP cc_start: 0.7207 (m-30) cc_final: 0.6998 (m-30)
REVERT: J  807 MET cc_start: 0.6494 (mmm) cc_final: 0.5574 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.2106
  time to fit residues: 33.4832
Evaluate side-chains
  116 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 21 optimal weight:    0.4980
   chunk 42 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** D 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 854 GLN
E 139 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.176246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.165917 restraints weight = 9385.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.4128 rms_B_bonded: 1.56
r_work: 0.4042 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3915 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6630
moved from start:          0.1392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   6845  Z= 0.263
  Angle     :  0.671   8.547   9217  Z= 0.365
  Chirality :  0.044   0.181   1041
  Planarity :  0.005   0.067   1219
  Dihedral  :  5.500  27.507    981
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  :  9.17 %
    Favored  : 88.40 %
  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: -0.47 (0.29), residues: 852
  helix:  0.86 (0.26), residues: 381
  sheet: -2.10 (0.31), residues: 226
  loop :  0.01 (0.43), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP C 827 
 HIS   0.006   0.002   HIS B 350 
 PHE   0.006   0.001   PHE D 840 
 TYR   0.015   0.002   TYR C  13 
 ARG   0.007   0.001   ARG E 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05404 (  459)
  hydrogen bonds       : angle       5.95727 ( 1293)
  SS BOND              : bond        0.00323 (    4)
  SS BOND              : angle       1.42459 (    8)
  covalent geometry    : bond        0.00574 ( 6841)
  covalent geometry    : angle       0.67020 ( 9209)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.784 
Fit side-chains
REVERT: D  839 ARG cc_start: 0.7981 (ttp-110) cc_final: 0.7729 (ttp-110)
REVERT: C  865 VAL cc_start: 0.8132 (m) cc_final: 0.7898 (p)
REVERT: F  143 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7156 (mt)
REVERT: H  426 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6964 (mt-10)
REVERT: I  817 GLN cc_start: 0.7023 (mp10) cc_final: 0.6632 (mp10)
REVERT: I  862 ASP cc_start: 0.7514 (m-30) cc_final: 0.7103 (m-30)
REVERT: J  807 MET cc_start: 0.7833 (mmm) cc_final: 0.7527 (mmp)
  outliers start: 17
  outliers final: 9
  residues processed: 114
  average time/residue: 0.2133
  time to fit residues: 32.0061
Evaluate side-chains
  120 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain D residue  834 ASP
Chi-restraints excluded: chain C residue  798 SER
Chi-restraints excluded: chain C residue  821 VAL
Chi-restraints excluded: chain C residue  827 TRP
Chi-restraints excluded: chain C residue  836 VAL
Chi-restraints excluded: chain C residue  846 SER
Chi-restraints excluded: chain F residue  143 ILE
Chi-restraints excluded: chain I residue  821 VAL
Chi-restraints excluded: chain J residue  833 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 54 optimal weight:    0.4980
   chunk 28 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   chunk 31 optimal weight:    0.1980
   chunk 49 optimal weight:    0.4980
   chunk 64 optimal weight:    0.5980
   chunk 59 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
C 854 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.178902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.168470 restraints weight = 9431.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.4149 rms_B_bonded: 1.57
r_work: 0.4061 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3934 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6599
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6845  Z= 0.177
  Angle     :  0.546   5.694   9217  Z= 0.301
  Chirality :  0.040   0.153   1041
  Planarity :  0.004   0.059   1219
  Dihedral  :  5.039  21.685    981
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 13.32 %
    Favored  : 84.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.30), residues: 852
  helix:  1.49 (0.26), residues: 385
  sheet: -1.87 (0.31), residues: 244
  loop :  0.25 (0.46), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP I 827 
 HIS   0.003   0.001   HIS A 350 
 PHE   0.004   0.001   PHE I 840 
 TYR   0.014   0.002   TYR C  13 
 ARG   0.008   0.000   ARG F 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04655 (  459)
  hydrogen bonds       : angle       5.39579 ( 1293)
  SS BOND              : bond        0.00207 (    4)
  SS BOND              : angle       0.97543 (    8)
  covalent geometry    : bond        0.00379 ( 6841)
  covalent geometry    : angle       0.54564 ( 9209)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.781 
Fit side-chains
REVERT: A  350 HIS cc_start: 0.3751 (OUTLIER) cc_final: 0.3300 (m-70)
REVERT: B  397 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7433 (tp30)
REVERT: E  139 ASN cc_start: 0.6251 (t0) cc_final: 0.5742 (t0)
REVERT: F  143 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.7101 (mt)
REVERT: H  426 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6854 (mt-10)
REVERT: I  817 GLN cc_start: 0.6898 (mp10) cc_final: 0.6538 (mp10)
REVERT: I  862 ASP cc_start: 0.7323 (m-30) cc_final: 0.6992 (m-30)
REVERT: J  807 MET cc_start: 0.7880 (mmm) cc_final: 0.7474 (mmm)
REVERT: J  810 TYR cc_start: 0.6542 (m-80) cc_final: 0.6268 (m-80)
REVERT: J  859 LYS cc_start: 0.7133 (mtmm) cc_final: 0.6872 (mtmm)
  outliers start: 18
  outliers final: 6
  residues processed: 117
  average time/residue: 0.2126
  time to fit residues: 32.8012
Evaluate side-chains
  118 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 HIS
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain C residue  798 SER
Chi-restraints excluded: chain C residue  821 VAL
Chi-restraints excluded: chain C residue  827 TRP
Chi-restraints excluded: chain C residue  836 VAL
Chi-restraints excluded: chain C residue  846 SER
Chi-restraints excluded: chain F residue  143 ILE
Chi-restraints excluded: chain I residue  821 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 76 optimal weight:    0.7980
   chunk 64 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0770
   chunk 46 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 61 optimal weight:    0.0770
   chunk 65 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.4696

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

Flipped N/Q/H residues before XYZ refinement:
C 854 GLN
I 883 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.178728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.168675 restraints weight = 9415.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.4165 rms_B_bonded: 1.52
r_work: 0.4080 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3952 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6588
moved from start:          0.2059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6845  Z= 0.173
  Angle     :  0.529   5.372   9217  Z= 0.293
  Chirality :  0.040   0.144   1041
  Planarity :  0.004   0.053   1219
  Dihedral  :  4.917  22.982    981
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 15.19 %
    Favored  : 82.81 %
  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:  0.47 (0.30), residues: 852
  helix:  1.85 (0.25), residues: 382
  sheet: -1.78 (0.31), residues: 243
  loop :  0.43 (0.46), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 878 
 HIS   0.003   0.001   HIS B 350 
 PHE   0.005   0.001   PHE I 840 
 TYR   0.013   0.002   TYR C  13 
 ARG   0.009   0.000   ARG B 404 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04421 (  459)
  hydrogen bonds       : angle       5.18730 ( 1293)
  SS BOND              : bond        0.00212 (    4)
  SS BOND              : angle       0.95763 (    8)
  covalent geometry    : bond        0.00372 ( 6841)
  covalent geometry    : angle       0.52896 ( 9209)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
REVERT: A  350 HIS cc_start: 0.3742 (OUTLIER) cc_final: 0.3101 (m-70)
REVERT: E  128 ARG cc_start: 0.5988 (ttm110) cc_final: 0.5777 (ttm170)
REVERT: E  139 ASN cc_start: 0.6165 (t0) cc_final: 0.5923 (t0)
REVERT: F  143 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.7014 (mt)
REVERT: H  426 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6818 (mt-10)
REVERT: J  810 TYR cc_start: 0.6687 (m-80) cc_final: 0.6451 (m-80)
  outliers start: 14
  outliers final: 7
  residues processed: 115
  average time/residue: 0.2084
  time to fit residues: 31.5649
Evaluate side-chains
  118 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 HIS
Chi-restraints excluded: chain C residue  798 SER
Chi-restraints excluded: chain C residue  821 VAL
Chi-restraints excluded: chain C residue  827 TRP
Chi-restraints excluded: chain C residue  836 VAL
Chi-restraints excluded: chain C residue  846 SER
Chi-restraints excluded: chain F residue  143 ILE
Chi-restraints excluded: chain I residue  821 VAL
Chi-restraints excluded: chain J residue  833 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 28 optimal weight:    0.5980
   chunk 72 optimal weight:    0.8980
   chunk 58 optimal weight:    0.0670
   chunk 13 optimal weight:    0.4980
   chunk 17 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0970
   chunk 66 optimal weight:    0.3980
   chunk 23 optimal weight:    0.3980
   chunk 33 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.2916

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

Flipped N/Q/H residues before XYZ refinement:
C 854 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.183935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.172071 restraints weight = 9340.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.4202 rms_B_bonded: 1.88
r_work: 0.4101 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3958 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6604
moved from start:          0.2411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6845  Z= 0.129
  Angle     :  0.476   5.230   9217  Z= 0.265
  Chirality :  0.038   0.136   1041
  Planarity :  0.003   0.049   1219
  Dihedral  :  4.570  21.110    981
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 15.47 %
    Favored  : 81.52 %
  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:  0.98 (0.30), residues: 852
  helix:  2.38 (0.25), residues: 379
  sheet: -1.66 (0.31), residues: 246
  loop :  0.68 (0.47), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 878 
 HIS   0.002   0.001   HIS A 350 
 PHE   0.006   0.001   PHE I 840 
 TYR   0.010   0.001   TYR C  13 
 ARG   0.004   0.000   ARG E 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04019 (  459)
  hydrogen bonds       : angle       4.80322 ( 1293)
  SS BOND              : bond        0.00135 (    4)
  SS BOND              : angle       0.64198 (    8)
  covalent geometry    : bond        0.00270 ( 6841)
  covalent geometry    : angle       0.47546 ( 9209)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
REVERT: C  831 ASN cc_start: 0.7429 (OUTLIER) cc_final: 0.7057 (m110)
REVERT: E  128 ARG cc_start: 0.6031 (ttm110) cc_final: 0.5798 (ttm170)
REVERT: J  807 MET cc_start: 0.8036 (mmm) cc_final: 0.7751 (mmm)
REVERT: J  810 TYR cc_start: 0.6689 (m-80) cc_final: 0.6441 (m-80)
  outliers start: 21
  outliers final: 9
  residues processed: 117
  average time/residue: 0.2060
  time to fit residues: 31.6729
Evaluate side-chains
  118 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue  798 SER
Chi-restraints excluded: chain C residue  821 VAL
Chi-restraints excluded: chain C residue  827 TRP
Chi-restraints excluded: chain C residue  831 ASN
Chi-restraints excluded: chain C residue  846 SER
Chi-restraints excluded: chain C residue  886 VAL
Chi-restraints excluded: chain E residue  122 LEU
Chi-restraints excluded: chain J residue  823 VAL
Chi-restraints excluded: chain J residue  833 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 61 optimal weight:    0.4980
   chunk 6 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 9 optimal weight:    0.4980
   chunk 58 optimal weight:    0.0060
   chunk 77 optimal weight:    0.0670
   chunk 36 optimal weight:    0.0770
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.2292

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

Flipped N/Q/H residues before XYZ refinement:
** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 854 GLN
E 139 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.185209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.173248 restraints weight = 9403.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.4215 rms_B_bonded: 1.91
r_work: 0.4114 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3972 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6583
moved from start:          0.2654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6845  Z= 0.115
  Angle     :  0.460   5.401   9217  Z= 0.257
  Chirality :  0.038   0.133   1041
  Planarity :  0.003   0.046   1219
  Dihedral  :  4.356  21.771    981
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 17.48 %
    Favored  : 79.66 %
  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:  1.27 (0.30), residues: 852
  helix:  2.60 (0.25), residues: 383
  sheet: -1.53 (0.30), residues: 253
  loop :  0.92 (0.50), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 878 
 HIS   0.002   0.001   HIS B 350 
 PHE   0.006   0.001   PHE I 840 
 TYR   0.009   0.001   TYR C  13 
 ARG   0.005   0.000   ARG B 404 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03858 (  459)
  hydrogen bonds       : angle       4.61549 ( 1293)
  SS BOND              : bond        0.00084 (    4)
  SS BOND              : angle       0.56573 (    8)
  covalent geometry    : bond        0.00235 ( 6841)
  covalent geometry    : angle       0.46001 ( 9209)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.805 
Fit side-chains
REVERT: A  350 HIS cc_start: 0.3262 (OUTLIER) cc_final: 0.2992 (m-70)
REVERT: B  397 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7527 (tp30)
REVERT: C  831 ASN cc_start: 0.7357 (OUTLIER) cc_final: 0.7002 (m110)
REVERT: E  139 ASN cc_start: 0.5909 (OUTLIER) cc_final: 0.5693 (t0)
REVERT: I  851 VAL cc_start: 0.7568 (OUTLIER) cc_final: 0.7303 (m)
REVERT: I  872 TYR cc_start: 0.8542 (t80) cc_final: 0.8236 (t80)
REVERT: J  807 MET cc_start: 0.8025 (mmm) cc_final: 0.7808 (mmm)
REVERT: J  810 TYR cc_start: 0.6754 (m-80) cc_final: 0.6404 (m-80)
  outliers start: 20
  outliers final: 10
  residues processed: 115
  average time/residue: 0.2073
  time to fit residues: 31.6266
Evaluate side-chains
  118 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 HIS
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue  798 SER
Chi-restraints excluded: chain C residue  821 VAL
Chi-restraints excluded: chain C residue  827 TRP
Chi-restraints excluded: chain C residue  831 ASN
Chi-restraints excluded: chain C residue  835 SER
Chi-restraints excluded: chain C residue  846 SER
Chi-restraints excluded: chain C residue  886 VAL
Chi-restraints excluded: chain E residue  122 LEU
Chi-restraints excluded: chain E residue  139 ASN
Chi-restraints excluded: chain I residue  851 VAL
Chi-restraints excluded: chain J residue  823 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 63 optimal weight:    0.2980
   chunk 73 optimal weight:    0.0370
   chunk 41 optimal weight:    0.3980
   chunk 19 optimal weight:    0.6980
   chunk 67 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0370
   chunk 79 optimal weight:    0.9980
   overall best weight:    0.2736

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

Flipped N/Q/H residues before XYZ refinement:
** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 854 GLN
E 139 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.185152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.173126 restraints weight = 9296.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.4215 rms_B_bonded: 1.90
r_work: 0.4110 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3965 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6599
moved from start:          0.2695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6845  Z= 0.123
  Angle     :  0.462   5.618   9217  Z= 0.258
  Chirality :  0.038   0.133   1041
  Planarity :  0.003   0.045   1219
  Dihedral  :  4.327  20.071    981
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 17.48 %
    Favored  : 79.37 %
  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:  1.40 (0.31), residues: 852
  helix:  2.71 (0.25), residues: 383
  sheet: -1.44 (0.31), residues: 253
  loop :  0.93 (0.50), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 809 
 HIS   0.001   0.001   HIS B 350 
 PHE   0.006   0.001   PHE I 840 
 TYR   0.009   0.001   TYR C  13 
 ARG   0.007   0.000   ARG B 404 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03862 (  459)
  hydrogen bonds       : angle       4.58051 ( 1293)
  SS BOND              : bond        0.00082 (    4)
  SS BOND              : angle       0.61937 (    8)
  covalent geometry    : bond        0.00255 ( 6841)
  covalent geometry    : angle       0.46219 ( 9209)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.723 
Fit side-chains
REVERT: A  350 HIS cc_start: 0.3521 (OUTLIER) cc_final: 0.3285 (m-70)
REVERT: B  367 LEU cc_start: 0.7899 (mp) cc_final: 0.7659 (mt)
REVERT: C  831 ASN cc_start: 0.7386 (OUTLIER) cc_final: 0.7088 (m110)
REVERT: E  139 ASN cc_start: 0.5755 (OUTLIER) cc_final: 0.5550 (t0)
REVERT: H  420 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7574 (mt)
REVERT: I  851 VAL cc_start: 0.7572 (OUTLIER) cc_final: 0.7297 (m)
REVERT: I  872 TYR cc_start: 0.8543 (t80) cc_final: 0.8189 (t80)
REVERT: J  807 MET cc_start: 0.8060 (mmm) cc_final: 0.7834 (mmm)
REVERT: J  810 TYR cc_start: 0.6777 (m-80) cc_final: 0.6358 (m-80)
  outliers start: 22
  outliers final: 10
  residues processed: 114
  average time/residue: 0.1965
  time to fit residues: 29.6993
Evaluate side-chains
  115 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 HIS
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue  798 SER
Chi-restraints excluded: chain C residue  821 VAL
Chi-restraints excluded: chain C residue  827 TRP
Chi-restraints excluded: chain C residue  831 ASN
Chi-restraints excluded: chain C residue  835 SER
Chi-restraints excluded: chain C residue  846 SER
Chi-restraints excluded: chain C residue  886 VAL
Chi-restraints excluded: chain E residue  122 LEU
Chi-restraints excluded: chain E residue  139 ASN
Chi-restraints excluded: chain H residue  420 ILE
Chi-restraints excluded: chain I residue  851 VAL
Chi-restraints excluded: chain J residue  823 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0970
   chunk 75 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 68 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0870
   chunk 25 optimal weight:    0.4980
   chunk 29 optimal weight:    0.9990
   chunk 70 optimal weight:    0.3980
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.3356

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

Flipped N/Q/H residues before XYZ refinement:
** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 854 GLN
E 139 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.184411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.172287 restraints weight = 9458.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.4208 rms_B_bonded: 1.92
r_work: 0.4101 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3955 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6618
moved from start:          0.2705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6845  Z= 0.136
  Angle     :  0.473   5.848   9217  Z= 0.263
  Chirality :  0.038   0.135   1041
  Planarity :  0.003   0.044   1219
  Dihedral  :  4.393  22.745    981
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 18.48 %
    Favored  : 78.65 %
  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:  1.40 (0.30), residues: 852
  helix:  2.71 (0.25), residues: 387
  sheet: -1.39 (0.31), residues: 250
  loop :  0.80 (0.50), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP J 809 
 HIS   0.002   0.001   HIS B 350 
 PHE   0.006   0.001   PHE I 840 
 TYR   0.010   0.001   TYR C  13 
 ARG   0.006   0.000   ARG B 404 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03924 (  459)
  hydrogen bonds       : angle       4.60933 ( 1293)
  SS BOND              : bond        0.00125 (    4)
  SS BOND              : angle       0.76240 (    8)
  covalent geometry    : bond        0.00287 ( 6841)
  covalent geometry    : angle       0.47243 ( 9209)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.724 
Fit side-chains
REVERT: A  350 HIS cc_start: 0.3565 (OUTLIER) cc_final: 0.3274 (m-70)
REVERT: B  367 LEU cc_start: 0.7925 (mp) cc_final: 0.7688 (mt)
REVERT: I  851 VAL cc_start: 0.7601 (OUTLIER) cc_final: 0.7331 (m)
REVERT: I  872 TYR cc_start: 0.8560 (t80) cc_final: 0.8230 (t80)
REVERT: J  807 MET cc_start: 0.8079 (mmm) cc_final: 0.7852 (mmm)
REVERT: J  810 TYR cc_start: 0.6827 (m-80) cc_final: 0.6388 (m-80)
REVERT: J  859 LYS cc_start: 0.7205 (mtmm) cc_final: 0.7002 (mtmm)
  outliers start: 20
  outliers final: 13
  residues processed: 117
  average time/residue: 0.2068
  time to fit residues: 32.2794
Evaluate side-chains
  119 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 HIS
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue  798 SER
Chi-restraints excluded: chain C residue  821 VAL
Chi-restraints excluded: chain C residue  827 TRP
Chi-restraints excluded: chain C residue  835 SER
Chi-restraints excluded: chain C residue  846 SER
Chi-restraints excluded: chain C residue  851 VAL
Chi-restraints excluded: chain E residue  122 LEU
Chi-restraints excluded: chain I residue  851 VAL
Chi-restraints excluded: chain J residue  798 SER
Chi-restraints excluded: chain J residue  823 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 43 optimal weight:    0.5980
   chunk 76 optimal weight:    0.0040
   chunk 25 optimal weight:    0.0980
   chunk 23 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 80 optimal weight:    0.6980
   chunk 77 optimal weight:    0.3980
   chunk 13 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9990
   chunk 9 optimal weight:    0.4980
   chunk 52 optimal weight:    0.4980
   overall best weight:    0.2992

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

Flipped N/Q/H residues before XYZ refinement:
** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 854 GLN
E 139 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.185167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.173013 restraints weight = 9450.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.4210 rms_B_bonded: 1.92
r_work: 0.4104 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3960 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6599
moved from start:          0.2811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6845  Z= 0.129
  Angle     :  0.476   5.991   9217  Z= 0.261
  Chirality :  0.038   0.137   1041
  Planarity :  0.003   0.044   1219
  Dihedral  :  4.349  20.781    981
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 18.19 %
    Favored  : 78.65 %
  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:  1.38 (0.30), residues: 852
  helix:  2.59 (0.25), residues: 393
  sheet: -1.34 (0.31), residues: 250
  loop :  0.87 (0.51), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP J 809 
 HIS   0.002   0.001   HIS B 350 
 PHE   0.006   0.001   PHE I 840 
 TYR   0.009   0.001   TYR C  13 
 ARG   0.006   0.000   ARG B 404 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03894 (  459)
  hydrogen bonds       : angle       4.55938 ( 1293)
  SS BOND              : bond        0.00113 (    4)
  SS BOND              : angle       0.70358 (    8)
  covalent geometry    : bond        0.00273 ( 6841)
  covalent geometry    : angle       0.47564 ( 9209)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.778 
Fit side-chains
REVERT: A  350 HIS cc_start: 0.3550 (OUTLIER) cc_final: 0.3262 (m-70)
REVERT: B  397 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7139 (tp30)
REVERT: H  429 LEU cc_start: 0.8364 (mm) cc_final: 0.8058 (mp)
REVERT: I  851 VAL cc_start: 0.7557 (OUTLIER) cc_final: 0.7286 (m)
REVERT: I  872 TYR cc_start: 0.8549 (t80) cc_final: 0.8225 (t80)
REVERT: J  807 MET cc_start: 0.8061 (mmm) cc_final: 0.7827 (mmm)
REVERT: J  810 TYR cc_start: 0.6813 (m-80) cc_final: 0.6335 (m-80)
REVERT: J  859 LYS cc_start: 0.6965 (mtmm) cc_final: 0.6750 (mtmm)
  outliers start: 22
  outliers final: 14
  residues processed: 113
  average time/residue: 0.1987
  time to fit residues: 29.6283
Evaluate side-chains
  116 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 HIS
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  446 MET
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue  798 SER
Chi-restraints excluded: chain C residue  821 VAL
Chi-restraints excluded: chain C residue  827 TRP
Chi-restraints excluded: chain C residue  835 SER
Chi-restraints excluded: chain C residue  846 SER
Chi-restraints excluded: chain C residue  851 VAL
Chi-restraints excluded: chain C residue  886 VAL
Chi-restraints excluded: chain E residue  122 LEU
Chi-restraints excluded: chain I residue  851 VAL
Chi-restraints excluded: chain J residue  798 SER
Chi-restraints excluded: chain J residue  823 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 45 optimal weight:    0.1980
   chunk 24 optimal weight:    0.0270
   chunk 32 optimal weight:    0.4980
   chunk 18 optimal weight:    0.9990
   chunk 64 optimal weight:    0.0870
   chunk 2 optimal weight:    0.0070
   chunk 77 optimal weight:    0.3980
   chunk 69 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.1434

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

Flipped N/Q/H residues before XYZ refinement:
D 869 ASN
C 854 GLN
E 139 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.187562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.175246 restraints weight = 9568.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.4233 rms_B_bonded: 1.95
r_work: 0.4130 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3985 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6543
moved from start:          0.3147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6845  Z= 0.101
  Angle     :  0.452   6.574   9217  Z= 0.249
  Chirality :  0.037   0.134   1041
  Planarity :  0.003   0.043   1219
  Dihedral  :  4.079  18.804    981
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 19.20 %
    Favored  : 78.37 %
  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:  1.65 (0.31), residues: 852
  helix:  2.82 (0.25), residues: 396
  sheet: -1.21 (0.31), residues: 250
  loop :  0.91 (0.51), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP J 809 
 HIS   0.001   0.000   HIS A 350 
 PHE   0.005   0.001   PHE I 840 
 TYR   0.007   0.001   TYR D 872 
 ARG   0.005   0.000   ARG B 404 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03672 (  459)
  hydrogen bonds       : angle       4.33695 ( 1293)
  SS BOND              : bond        0.00064 (    4)
  SS BOND              : angle       0.42779 (    8)
  covalent geometry    : bond        0.00202 ( 6841)
  covalent geometry    : angle       0.45215 ( 9209)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.691 
Fit side-chains
REVERT: B  397 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7127 (tp30)
REVERT: E  129 ARG cc_start: 0.7226 (tpp80) cc_final: 0.6843 (ttm-80)
REVERT: E  139 ASN cc_start: 0.5928 (OUTLIER) cc_final: 0.5679 (t0)
REVERT: G  415 GLU cc_start: 0.7184 (tp30) cc_final: 0.6914 (tp30)
REVERT: H  426 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7050 (mt-10)
REVERT: H  429 LEU cc_start: 0.8338 (mm) cc_final: 0.8085 (mp)
REVERT: I  851 VAL cc_start: 0.7468 (OUTLIER) cc_final: 0.7167 (m)
REVERT: I  872 TYR cc_start: 0.8450 (t80) cc_final: 0.8123 (t80)
REVERT: I  878 TRP cc_start: 0.7518 (m100) cc_final: 0.7280 (m100)
REVERT: J  798 SER cc_start: 0.8258 (OUTLIER) cc_final: 0.8009 (m)
REVERT: J  807 MET cc_start: 0.8088 (mmm) cc_final: 0.7857 (mmm)
REVERT: J  809 TRP cc_start: 0.8110 (m100) cc_final: 0.7710 (m100)
REVERT: J  810 TYR cc_start: 0.6680 (m-80) cc_final: 0.6184 (m-80)
  outliers start: 17
  outliers final: 11
  residues processed: 114
  average time/residue: 0.2006
  time to fit residues: 29.8006
Evaluate side-chains
  118 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  446 MET
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue  798 SER
Chi-restraints excluded: chain C residue  821 VAL
Chi-restraints excluded: chain C residue  827 TRP
Chi-restraints excluded: chain C residue  846 SER
Chi-restraints excluded: chain C residue  886 VAL
Chi-restraints excluded: chain E residue  122 LEU
Chi-restraints excluded: chain E residue  139 ASN
Chi-restraints excluded: chain I residue  851 VAL
Chi-restraints excluded: chain J residue  798 SER
Chi-restraints excluded: chain J residue  823 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 26 optimal weight:    0.3980
   chunk 11 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0970
   chunk 5 optimal weight:    0.7980
   chunk 42 optimal weight:    0.4980
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
C 854 GLN
E 139 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.186055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.174410 restraints weight = 9405.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.4235 rms_B_bonded: 1.79
r_work: 0.4132 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3991 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6600
moved from start:          0.2902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6845  Z= 0.171
  Angle     :  0.524   6.927   9217  Z= 0.287
  Chirality :  0.039   0.135   1041
  Planarity :  0.004   0.074   1219
  Dihedral  :  4.439  22.252    981
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 19.63 %
    Favored  : 77.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.30), residues: 852
  helix:  2.60 (0.24), residues: 395
  sheet: -1.27 (0.31), residues: 250
  loop :  0.81 (0.51), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP J 809 
 HIS   0.006   0.001   HIS A 350 
 PHE   0.006   0.001   PHE I 840 
 TYR   0.013   0.002   TYR C  13 
 ARG   0.009   0.000   ARG F 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04025 (  459)
  hydrogen bonds       : angle       4.62396 ( 1293)
  SS BOND              : bond        0.00222 (    4)
  SS BOND              : angle       1.05992 (    8)
  covalent geometry    : bond        0.00374 ( 6841)
  covalent geometry    : angle       0.52298 ( 9209)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4037.20 seconds
wall clock time: 69 minutes 52.96 seconds (4192.96 seconds total)