Starting phenix.real_space_refine
on Tue May 13 17:52:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8whb_37538/05_2025/8whb_37538.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8whb_37538/05_2025/8whb_37538.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8whb_37538/05_2025/8whb_37538.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8whb_37538/05_2025/8whb_37538.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8whb_37538/05_2025/8whb_37538.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8whb_37538/05_2025/8whb_37538.cif"
  }
  resolution = 3.17
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     268      5.49       5
     S      12      5.16       5
     C    6211      2.51       5
     N    2067      2.21       5
     O    2618      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 11176
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 733
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 733
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 2, 'TRANS': 88}
    Chain: "B"
      Number of atoms: 636
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 636
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "C"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 783
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "D"
      Number of atoms: 694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 694
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 3, 'TRANS': 85}
    Chain: "E"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 799
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 621
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 621
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 1, 'TRANS': 75}
    Chain: "G"
      Number of atoms: 700
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 700
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 4, 'TRANS': 88}
    Chain: "H"
      Number of atoms: 716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 716
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 3, 'TRANS': 88}
    Chain: "I"
      Number of atoms: 2729
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 134, 2729
          Classifications: {'DNA': 134}
          Link IDs: {'rna3p': 133}
    Chain: "J"
      Number of atoms: 2765
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 134, 2765
          Classifications: {'DNA': 134}
          Link IDs: {'rna3p': 133}
  Time building chain proxies: 7.37, per 1000 atoms: 0.66
  Number of scatterers: 11176
  At special positions: 0
  Unit cell: (118.845, 101.745, 127.395, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      12     16.00
     P     268     15.00
     O    2618      8.00
     N    2067      7.00
     C    6211      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.80
  Conformation dependent library (CDL) restraints added in 722.8 milliseconds
  

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1352

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 10 sheets defined
      74.4% alpha, 3.3% beta
      86 base pairs and 224 stacking pairs defined.
    Time for finding SS restraints: 5.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.668A  pdb=" N   LEU A  48 " --> pdb=" O   GLY A  44 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ARG A  49 " --> pdb=" O   THR A  45 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   GLN A  55 " --> pdb=" O   ILE A  51 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 74
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.639A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA A  90 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ASP A 106 " --> pdb=" O   GLY A 102 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   LEU A 109 " --> pdb=" O   GLU A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.747A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.697A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LYS B  59 " --> pdb=" O   ARG B  55 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ILE B  60 " --> pdb=" O   GLY B  56 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   PHE B  61 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.909A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 23
    Processing helix  chain 'C' and resid 27 through 37
    Processing helix  chain 'C' and resid 47 through 74
    Processing helix  chain 'C' and resid 80 through 91
    Processing helix  chain 'C' and resid 91 through 98
    Processing helix  chain 'C' and resid 113 through 117
      removed outlier: 3.966A  pdb=" N   LEU C 117 " --> pdb=" O   ASN C 114 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 74
    Processing helix  chain 'D' and resid 80 through 109
      removed outlier: 3.736A  pdb=" N   ASN D 109 " --> pdb=" O   LEU D 105 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 115 through 127
      removed outlier: 3.732A  pdb=" N   ILE D 119 " --> pdb=" O   THR D 115 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   GLN D 120 " --> pdb=" O   SER D 116 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 128 through 149
      removed outlier: 3.743A  pdb=" N   SER D 137 " --> pdb=" O   LYS D 133 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 45 through 55
      removed outlier: 3.606A  pdb=" N   ARG E  49 " --> pdb=" O   THR E  45 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 76
      removed outlier: 3.586A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.791A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ALA E  90 " --> pdb=" O   SER E  86 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ALA E  98 " --> pdb=" O   GLU E  94 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   TYR E  99 " --> pdb=" O   ALA E  95 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLY E 102 " --> pdb=" O   ALA E  98 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ASP E 106 " --> pdb=" O   GLY E 102 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   LEU E 109 " --> pdb=" O   GLU E 105 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ILE E 112 " --> pdb=" O   ASN E 108 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 130
      removed outlier: 3.804A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.871A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   ARG F  55 " --> pdb=" O   TYR F  51 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   GLY F  56 " --> pdb=" O   GLU F  52 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   LYS F  59 " --> pdb=" O   ARG F  55 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ARG F  67 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   THR F  73 " --> pdb=" O   ALA F  69 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 3.689A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 27 through 38
    Processing helix  chain 'G' and resid 46 through 74
      removed outlier: 4.452A  pdb=" N   VAL G  50 " --> pdb=" O   ALA G  46 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LEU G  59 " --> pdb=" O   VAL G  55 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LEU G  66 " --> pdb=" O   GLU G  62 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ASN G  74 " --> pdb=" O   ALA G  70 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 80 through 91
      removed outlier: 3.602A  pdb=" N   ASP G  91 " --> pdb=" O   ALA G  87 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 98
    Processing helix  chain 'H' and resid 62 through 74
    Processing helix  chain 'H' and resid 80 through 109
      removed outlier: 3.786A  pdb=" N   ASN H 109 " --> pdb=" O   LEU H 105 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 116 through 127
      removed outlier: 3.879A  pdb=" N   THR H 121 " --> pdb=" O   ARG H 117 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 128 through 148
      removed outlier: 3.667A  pdb=" N   ALA H 132 " --> pdb=" O   PRO H 128 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   HIS H 134 " --> pdb=" O   GLU H 130 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   SER H 137 " --> pdb=" O   LYS H 133 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.960A  pdb=" N   ARG A  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 46
      removed outlier: 7.545A  pdb=" N   ARG B  45 " --> pdb=" O   ILE E 119 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 81
    Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 98
      removed outlier: 7.000A  pdb=" N   THR B  96 " --> pdb=" O   THR C 102 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 43 through 44
      removed outlier: 7.449A  pdb=" N   ARG C  43 " --> pdb=" O   ILE D 114 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'C' and resid 78 through 79
    Processing sheet with id=AA8, first strand: chain 'F' and resid 96 through 98
      removed outlier: 6.609A  pdb=" N   THR F  96 " --> pdb=" O   THR G 102 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44
      removed outlier: 7.158A  pdb=" N   ARG G  43 " --> pdb=" O   ILE H 114 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79

    359 hydrogen bonds defined for protein.
    1056 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      216 hydrogen bonds
      432 hydrogen bond angles
      0 basepair planarities
      86 basepair parallelities
      224 stacking parallelities
  Total time for adding SS restraints: 3.75

  Time building geometry restraints manager: 3.28 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1313
        1.32 -     1.44: 4203
        1.44 -     1.56: 5846
        1.56 -     1.68: 537
        1.68 -     1.80: 22
  Bond restraints: 11921
  Sorted by residual:
  bond pdb=" N   GLU F  52 "
       pdb=" CA  GLU F  52 "
    ideal  model  delta    sigma   weight residual
    1.455  1.504 -0.049 1.29e-02 6.01e+03 1.44e+01
  bond pdb=" NE  ARG C  89 "
       pdb=" CZ  ARG C  89 "
    ideal  model  delta    sigma   weight residual
    1.326  1.365 -0.039 1.10e-02 8.26e+03 1.27e+01
  bond pdb=" N   ILE F  26 "
       pdb=" CA  ILE F  26 "
    ideal  model  delta    sigma   weight residual
    1.459  1.503 -0.044 1.25e-02 6.40e+03 1.23e+01
  bond pdb=" N   GLN F  27 "
       pdb=" CA  GLN F  27 "
    ideal  model  delta    sigma   weight residual
    1.457  1.500 -0.043 1.35e-02 5.49e+03 1.02e+01
  bond pdb=" N   LYS F  59 "
       pdb=" CA  LYS F  59 "
    ideal  model  delta    sigma   weight residual
    1.459  1.499 -0.041 1.28e-02 6.10e+03 1.01e+01
  ... (remaining 11916 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.80: 16857
        2.80 -     5.59: 352
        5.59 -     8.39: 31
        8.39 -    11.19: 2
       11.19 -    13.98: 5
  Bond angle restraints: 17247
  Sorted by residual:
  angle pdb=" O3'  DT J   9 "
        pdb=" C3'  DT J   9 "
        pdb=" C2'  DT J   9 "
      ideal   model   delta    sigma   weight residual
     111.50  125.48  -13.98 1.50e+00 4.44e-01 8.69e+01
  angle pdb=" N   THR E 107 "
        pdb=" CA  THR E 107 "
        pdb=" C   THR E 107 "
      ideal   model   delta    sigma   weight residual
     113.18  102.29   10.89 1.21e+00 6.83e-01 8.10e+01
  angle pdb=" O3'  DA I 106 "
        pdb=" C3'  DA I 106 "
        pdb=" C2'  DA I 106 "
      ideal   model   delta    sigma   weight residual
     111.50  124.99  -13.49 1.50e+00 4.44e-01 8.09e+01
  angle pdb=" O3'  DG I 126 "
        pdb=" C3'  DG I 126 "
        pdb=" C2'  DG I 126 "
      ideal   model   delta    sigma   weight residual
     111.50  124.43  -12.93 1.50e+00 4.44e-01 7.43e+01
  angle pdb=" O3'  DT J  24 "
        pdb=" C3'  DT J  24 "
        pdb=" C2'  DT J  24 "
      ideal   model   delta    sigma   weight residual
     111.50  124.43  -12.93 1.50e+00 4.44e-01 7.43e+01
  ... (remaining 17242 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.91: 5232
       34.91 -    69.82: 1200
       69.82 -   104.74: 34
      104.74 -   139.65: 2
      139.65 -   174.56: 4
  Dihedral angle restraints: 6472
    sinusoidal: 4381
      harmonic: 2091
  Sorted by residual:
  dihedral pdb=" CA  GLU H 118 "
           pdb=" C   GLU H 118 "
           pdb=" N   ILE H 119 "
           pdb=" CA  ILE H 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.95   27.05     0      5.00e+00 4.00e-02 2.93e+01
  dihedral pdb=" CA  LEU E  60 "
           pdb=" C   LEU E  60 "
           pdb=" N   LEU E  61 "
           pdb=" CA  LEU E  61 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.21  -22.79     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" CA  GLU E 133 "
           pdb=" C   GLU E 133 "
           pdb=" N   ARG E 134 "
           pdb=" CA  ARG E 134 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.16   20.84     0      5.00e+00 4.00e-02 1.74e+01
  ... (remaining 6469 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.164: 1955
       0.164 -    0.329: 12
       0.329 -    0.493: 0
       0.493 -    0.657: 2
       0.657 -    0.821: 3
  Chirality restraints: 1972
  Sorted by residual:
  chirality pdb=" C3'  DG I 126 "
            pdb=" C4'  DG I 126 "
            pdb=" O3'  DG I 126 "
            pdb=" C2'  DG I 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -1.84   -0.82 2.00e-01 2.50e+01 1.69e+01
  chirality pdb=" C3'  DA I 106 "
            pdb=" C4'  DA I 106 "
            pdb=" O3'  DA I 106 "
            pdb=" C2'  DA I 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -1.94   -0.72 2.00e-01 2.50e+01 1.31e+01
  chirality pdb=" C3'  DT J  24 "
            pdb=" C4'  DT J  24 "
            pdb=" O3'  DT J  24 "
            pdb=" C2'  DT J  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -1.98   -0.68 2.00e-01 2.50e+01 1.15e+01
  ... (remaining 1969 not shown)

  Planarity restraints: 1249
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J  27 "    0.045 2.00e-02 2.50e+03   2.09e-02 9.82e+00
        pdb=" N1   DC J  27 "   -0.015 2.00e-02 2.50e+03
        pdb=" C2   DC J  27 "   -0.016 2.00e-02 2.50e+03
        pdb=" O2   DC J  27 "   -0.010 2.00e-02 2.50e+03
        pdb=" N3   DC J  27 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4   DC J  27 "    0.007 2.00e-02 2.50e+03
        pdb=" N4   DC J  27 "    0.025 2.00e-02 2.50e+03
        pdb=" C5   DC J  27 "   -0.010 2.00e-02 2.50e+03
        pdb=" C6   DC J  27 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP E 106 "   -0.015 2.00e-02 2.50e+03   3.02e-02 9.12e+00
        pdb=" C   ASP E 106 "    0.052 2.00e-02 2.50e+03
        pdb=" O   ASP E 106 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   THR E 107 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR F  51 "   -0.015 2.00e-02 2.50e+03   3.00e-02 9.01e+00
        pdb=" C   TYR F  51 "    0.052 2.00e-02 2.50e+03
        pdb=" O   TYR F  51 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   GLU F  52 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1246 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 2427
        2.80 -     3.32: 9588
        3.32 -     3.85: 20983
        3.85 -     4.37: 25240
        4.37 -     4.90: 35944
  Nonbonded interactions: 94182
  Sorted by model distance:
  nonbonded pdb=" O   ASP C  91 "
            pdb=" OG  SER C  95 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OH  TYR G  58 "
            pdb=" OE2 GLU G  62 "
     model   vdw
     2.335 3.040
  nonbonded pdb=" NE  ARG E 131 "
            pdb=" OE2 GLU E 133 "
     model   vdw
     2.342 3.120
  nonbonded pdb=" OH  TYR C  40 "
            pdb=" OE1 GLU D  96 "
     model   vdw
     2.415 3.040
  nonbonded pdb=" NH2 ARG E 131 "
            pdb=" OE2 GLU E 133 "
     model   vdw
     2.420 3.120
  ... (remaining 94177 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 'E' and resid 43 through 133)
}
ncs_group {
  reference = (chain 'B' and resid 24 through 100)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 18 through 110)
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'H' and resid 61 through 149)
}

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:             1.790
  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:          0.460
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     30.970
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.050
  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:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
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      :  0.007   0.059  11921  Z= 0.356
  Angle     :  1.006  13.981  17247  Z= 0.640
  Chirality :  0.060   0.821   1972
  Planarity :  0.006   0.055   1249
  Dihedral  : 27.902 174.559   5120
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.53 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.07 (0.29), residues: 707
  helix: -0.87 (0.22), residues: 510
  sheet:  None (None), residues: 0
  loop : -2.40 (0.37), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS G  83 
 PHE   0.049   0.003   PHE C  26 
 TYR   0.013   0.003   TYR H  65 
 ARG   0.010   0.001   ARG G  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20894 (  575)
  hydrogen bonds       : angle       7.77230 ( 1488)
  covalent geometry    : bond        0.00740 (11921)
  covalent geometry    : angle       1.00567 (17247)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.845 
Fit side-chains
REVERT: C  105 ASN cc_start: 0.8857 (t0) cc_final: 0.8656 (t0)
REVERT: C  111 ASN cc_start: 0.8084 (t0) cc_final: 0.7741 (p0)
REVERT: D  111 LYS cc_start: 0.8478 (mmtm) cc_final: 0.8191 (mtpt)
  outliers start: 0
  outliers final: 0
  residues processed: 202
  average time/residue: 0.3996
  time to fit residues: 98.8569
Evaluate side-chains
  152 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    6.9990
   chunk 71 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 24 optimal weight:    0.3980
   chunk 48 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 73 optimal weight:    5.9990
   chunk 28 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 85 optimal weight:    5.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
C  85 GLN
H  74 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.128163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.092666 restraints weight = 20881.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 1.56
r_work: 0.3090 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.2881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  11921  Z= 0.178
  Angle     :  0.626   8.805  17247  Z= 0.370
  Chirality :  0.037   0.258   1972
  Planarity :  0.005   0.045   1249
  Dihedral  : 30.961 176.787   3713
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 10.74 %
    Favored  : 87.58 %
  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:  0.19 (0.32), residues: 707
  helix:  0.88 (0.23), residues: 523
  sheet:  None (None), residues: 0
  loop : -2.01 (0.40), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.010   0.001   PHE B  61 
 TYR   0.008   0.001   TYR F  51 
 ARG   0.007   0.001   ARG H 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05130 (  575)
  hydrogen bonds       : angle       3.08309 ( 1488)
  covalent geometry    : bond        0.00383 (11921)
  covalent geometry    : angle       0.62631 (17247)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 165
  time to evaluate  : 0.798 
Fit side-chains
REVERT: B   84 MET cc_start: 0.8316 (mmm) cc_final: 0.8001 (mmt)
REVERT: C   18 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.7874 (mpp80)
REVERT: C   74 ASN cc_start: 0.7111 (m-40) cc_final: 0.6548 (t0)
REVERT: C   89 ARG cc_start: 0.8795 (mmt90) cc_final: 0.8574 (mmt180)
REVERT: C  105 ASN cc_start: 0.9019 (t0) cc_final: 0.8218 (t0)
REVERT: C  111 ASN cc_start: 0.8368 (t0) cc_final: 0.7850 (p0)
REVERT: D  111 LYS cc_start: 0.8473 (mmtm) cc_final: 0.8155 (mtpt)
REVERT: D  141 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8520 (ttpp)
REVERT: F   79 LYS cc_start: 0.9057 (mtpt) cc_final: 0.8787 (mtmt)
REVERT: H  104 LYS cc_start: 0.8466 (ttmt) cc_final: 0.7985 (ttmm)
  outliers start: 10
  outliers final: 2
  residues processed: 170
  average time/residue: 0.3555
  time to fit residues: 75.6364
Evaluate side-chains
  161 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 157
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   18 ARG
Chi-restraints excluded: chain D residue  141 LYS
Chi-restraints excluded: chain E residue   87 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 19 optimal weight:    6.9990
   chunk 93 optimal weight:   10.0000
   chunk 24 optimal weight:    0.0050
   chunk 77 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 71 optimal weight:    5.9990
   chunk 29 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 44 optimal weight:    0.8980
   overall best weight:    1.0796

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.118815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.081850 restraints weight = 20678.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3051 rms_B_bonded: 1.66
r_work: 0.2868 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.4237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11921  Z= 0.171
  Angle     :  0.577   6.994  17247  Z= 0.342
  Chirality :  0.035   0.158   1972
  Planarity :  0.004   0.041   1249
  Dihedral  : 30.820 178.375   3713
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 12.58 %
    Favored  : 84.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.32), residues: 707
  helix:  1.76 (0.23), residues: 523
  sheet:  None (None), residues: 0
  loop : -1.58 (0.42), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.019   0.001   PHE C  26 
 TYR   0.008   0.001   TYR D  62 
 ARG   0.006   0.000   ARG D 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04970 (  575)
  hydrogen bonds       : angle       2.75474 ( 1488)
  covalent geometry    : bond        0.00371 (11921)
  covalent geometry    : angle       0.57708 (17247)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 175
  time to evaluate  : 0.851 
Fit side-chains
REVERT: C   18 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8128 (mpp80)
REVERT: C   74 ASN cc_start: 0.7380 (m-40) cc_final: 0.6869 (t0)
REVERT: C   78 ARG cc_start: 0.8926 (mtm-85) cc_final: 0.8577 (mtm-85)
REVERT: C  105 ASN cc_start: 0.8921 (t0) cc_final: 0.8155 (t0)
REVERT: C  109 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7850 (mtm)
REVERT: C  111 ASN cc_start: 0.8458 (t0) cc_final: 0.7912 (p0)
REVERT: D  104 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7850 (mtmm)
REVERT: D  111 LYS cc_start: 0.8620 (mmtm) cc_final: 0.8129 (mtpt)
REVERT: F   79 LYS cc_start: 0.9099 (mtpt) cc_final: 0.8791 (mtmt)
REVERT: H   60 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7669 (pt0)
  outliers start: 15
  outliers final: 7
  residues processed: 181
  average time/residue: 0.3741
  time to fit residues: 84.2404
Evaluate side-chains
  166 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 156
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue   18 ARG
Chi-restraints excluded: chain C residue  109 MET
Chi-restraints excluded: chain D residue  104 LYS
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue  102 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 21 optimal weight:    6.9990
   chunk 78 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 1 optimal weight:    9.9990
   chunk 48 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 7 optimal weight:    0.4980
   chunk 43 optimal weight:    0.3980
   chunk 83 optimal weight:    8.9990
   chunk 77 optimal weight:    3.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
C  25 GLN
G  85 GLN
H 134 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.110592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.073525 restraints weight = 20578.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.2898 rms_B_bonded: 1.64
r_work: 0.2711 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8723
moved from start:          0.5180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  11921  Z= 0.233
  Angle     :  0.630   8.614  17247  Z= 0.369
  Chirality :  0.039   0.155   1972
  Planarity :  0.005   0.040   1249
  Dihedral  : 30.869 177.598   3713
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 12.58 %
    Favored  : 83.89 %
  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:  1.48 (0.32), residues: 707
  helix:  1.85 (0.23), residues: 520
  sheet:  None (None), residues: 0
  loop : -1.56 (0.41), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D  74 
 PHE   0.022   0.002   PHE C  26 
 TYR   0.011   0.001   TYR B  51 
 ARG   0.003   0.000   ARG B  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06206 (  575)
  hydrogen bonds       : angle       2.98555 ( 1488)
  covalent geometry    : bond        0.00538 (11921)
  covalent geometry    : angle       0.63043 (17247)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 163
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.8992 (tttm) cc_final: 0.8779 (tttt)
REVERT: C   18 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8268 (mpp80)
REVERT: C   73 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8291 (m-30)
REVERT: C   74 ASN cc_start: 0.8342 (m-40) cc_final: 0.7772 (t0)
REVERT: C  105 ASN cc_start: 0.9047 (t0) cc_final: 0.8299 (t0)
REVERT: C  111 ASN cc_start: 0.8460 (t0) cc_final: 0.8157 (p0)
REVERT: D   82 LYS cc_start: 0.8964 (mttt) cc_final: 0.8749 (mttm)
REVERT: D  104 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7995 (mtmm)
REVERT: D  111 LYS cc_start: 0.8825 (mmtm) cc_final: 0.8442 (mtpt)
REVERT: F   79 LYS cc_start: 0.9120 (mtpt) cc_final: 0.8795 (mtmt)
REVERT: H   63 LYS cc_start: 0.9098 (mptt) cc_final: 0.8889 (mptt)
REVERT: H   68 LYS cc_start: 0.9189 (ttmt) cc_final: 0.8872 (mttt)
REVERT: H  130 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7602 (tm-30)
  outliers start: 21
  outliers final: 11
  residues processed: 170
  average time/residue: 0.3702
  time to fit residues: 78.3436
Evaluate side-chains
  166 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 152
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue   18 ARG
Chi-restraints excluded: chain C residue   65 GLU
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue  109 MET
Chi-restraints excluded: chain D residue  104 LYS
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain G residue   77 THR
Chi-restraints excluded: chain G residue  102 THR
Chi-restraints excluded: chain H residue  147 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 87 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 70 optimal weight:    8.9990
   chunk 84 optimal weight:    7.9990
   chunk 7 optimal weight:    0.3980
   chunk 36 optimal weight:    1.9990
   chunk 79 optimal weight:    8.9990
   chunk 62 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  25 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.113170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.076866 restraints weight = 20617.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 1.61
r_work: 0.2783 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8651
moved from start:          0.5493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11921  Z= 0.161
  Angle     :  0.542   7.143  17247  Z= 0.324
  Chirality :  0.034   0.148   1972
  Planarity :  0.004   0.038   1249
  Dihedral  : 30.498 178.500   3713
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 13.76 %
    Favored  : 83.56 %
  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:  1.98 (0.33), residues: 707
  helix:  2.25 (0.23), residues: 523
  sheet:  None (None), residues: 0
  loop : -1.59 (0.42), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B  75 
 PHE   0.011   0.001   PHE C  26 
 TYR   0.006   0.001   TYR B  51 
 ARG   0.004   0.000   ARG D 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04447 (  575)
  hydrogen bonds       : angle       2.61229 ( 1488)
  covalent geometry    : bond        0.00356 (11921)
  covalent geometry    : angle       0.54208 (17247)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 153
  time to evaluate  : 0.857 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8492 (tt0) cc_final: 0.8267 (tt0)
REVERT: A   79 LYS cc_start: 0.8965 (tttm) cc_final: 0.8734 (tttt)
REVERT: B   74 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8549 (mt-10)
REVERT: C   18 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8278 (mpp80)
REVERT: C   73 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8126 (m-30)
REVERT: C   74 ASN cc_start: 0.7905 (m-40) cc_final: 0.7452 (t0)
REVERT: C  105 ASN cc_start: 0.9028 (t0) cc_final: 0.8204 (t0)
REVERT: C  109 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7997 (mtm)
REVERT: C  111 ASN cc_start: 0.8483 (t0) cc_final: 0.8264 (p0)
REVERT: D  104 LYS cc_start: 0.8087 (mptt) cc_final: 0.7882 (mtmm)
REVERT: D  111 LYS cc_start: 0.8701 (mmtm) cc_final: 0.8283 (mtpt)
REVERT: F   79 LYS cc_start: 0.9118 (mtpt) cc_final: 0.8887 (mttp)
REVERT: H   68 LYS cc_start: 0.9219 (ttmt) cc_final: 0.8904 (mttt)
REVERT: H  130 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7622 (tm-30)
  outliers start: 16
  outliers final: 9
  residues processed: 159
  average time/residue: 0.3731
  time to fit residues: 74.1961
Evaluate side-chains
  163 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 150
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue   18 ARG
Chi-restraints excluded: chain C residue   65 GLU
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue  109 MET
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain G residue   39 LYS
Chi-restraints excluded: chain G residue  102 THR
Chi-restraints excluded: chain H residue  147 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9980
   chunk 89 optimal weight:    5.9990
   chunk 58 optimal weight:   10.0000
   chunk 54 optimal weight:    0.9980
   chunk 57 optimal weight:    0.8980
   chunk 83 optimal weight:   10.0000
   chunk 90 optimal weight:    5.9990
   chunk 88 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   overall best weight:    1.5782

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
F  25 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.111565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.075069 restraints weight = 20790.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.2926 rms_B_bonded: 1.65
r_work: 0.2740 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8688
moved from start:          0.5697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11921  Z= 0.179
  Angle     :  0.553   7.442  17247  Z= 0.328
  Chirality :  0.035   0.150   1972
  Planarity :  0.004   0.036   1249
  Dihedral  : 30.457 177.893   3713
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 13.76 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.14 (0.33), residues: 707
  helix:  2.35 (0.23), residues: 524
  sheet:  None (None), residues: 0
  loop : -1.48 (0.42), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D  74 
 PHE   0.015   0.001   PHE C  26 
 TYR   0.009   0.001   TYR B  51 
 ARG   0.004   0.000   ARG D 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04963 (  575)
  hydrogen bonds       : angle       2.67774 ( 1488)
  covalent geometry    : bond        0.00403 (11921)
  covalent geometry    : angle       0.55258 (17247)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 160
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.8946 (tttm) cc_final: 0.8709 (tttt)
REVERT: C   18 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8177 (mpp80)
REVERT: C   73 ASP cc_start: 0.8458 (m-30) cc_final: 0.8161 (m-30)
REVERT: C   74 ASN cc_start: 0.7980 (m-40) cc_final: 0.7543 (t0)
REVERT: C  105 ASN cc_start: 0.9034 (t0) cc_final: 0.8191 (t0)
REVERT: C  109 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8033 (mtm)
REVERT: D  104 LYS cc_start: 0.8146 (mptt) cc_final: 0.7903 (mtmm)
REVERT: D  111 LYS cc_start: 0.8686 (mmtm) cc_final: 0.8264 (mtpt)
REVERT: F   79 LYS cc_start: 0.9102 (mtpt) cc_final: 0.8872 (mttp)
REVERT: H   68 LYS cc_start: 0.9184 (ttmt) cc_final: 0.8849 (mttt)
REVERT: H  130 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7638 (tm-30)
  outliers start: 15
  outliers final: 10
  residues processed: 166
  average time/residue: 0.3880
  time to fit residues: 81.3703
Evaluate side-chains
  171 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 159
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue   18 ARG
Chi-restraints excluded: chain C residue   65 GLU
Chi-restraints excluded: chain C residue  109 MET
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain G residue   39 LYS
Chi-restraints excluded: chain G residue  102 THR
Chi-restraints excluded: chain H residue  147 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 69 optimal weight:   10.0000
   chunk 53 optimal weight:    0.4980
   chunk 70 optimal weight:    7.9990
   chunk 76 optimal weight:    5.9990
   chunk 41 optimal weight:    0.1980
   chunk 8 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 75 optimal weight:    5.9990
   chunk 71 optimal weight:    5.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
F  25 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.112113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.075824 restraints weight = 21117.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.2937 rms_B_bonded: 1.65
r_work: 0.2754 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8679
moved from start:          0.5904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11921  Z= 0.174
  Angle     :  0.542   7.151  17247  Z= 0.324
  Chirality :  0.034   0.147   1972
  Planarity :  0.004   0.035   1249
  Dihedral  : 30.227 178.495   3713
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 15.10 %
    Favored  : 82.55 %
  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:  2.32 (0.33), residues: 707
  helix:  2.49 (0.23), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.41 (0.42), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D  74 
 PHE   0.013   0.001   PHE C  26 
 TYR   0.007   0.001   TYR H  65 
 ARG   0.003   0.000   ARG D 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04625 (  575)
  hydrogen bonds       : angle       2.59556 ( 1488)
  covalent geometry    : bond        0.00389 (11921)
  covalent geometry    : angle       0.54225 (17247)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 159
  time to evaluate  : 0.887 
Fit side-chains
REVERT: A   79 LYS cc_start: 0.8948 (tttm) cc_final: 0.8730 (tttt)
REVERT: B   74 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8537 (mt-10)
REVERT: C   18 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8169 (mpp80)
REVERT: C   73 ASP cc_start: 0.8467 (m-30) cc_final: 0.8225 (m-30)
REVERT: C   74 ASN cc_start: 0.7972 (m-40) cc_final: 0.7560 (t0)
REVERT: C  105 ASN cc_start: 0.9030 (t0) cc_final: 0.8170 (t0)
REVERT: C  109 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7996 (mtm)
REVERT: D  104 LYS cc_start: 0.8162 (mptt) cc_final: 0.7920 (mtmm)
REVERT: D  111 LYS cc_start: 0.8682 (mmtm) cc_final: 0.8272 (mtpt)
REVERT: H   68 LYS cc_start: 0.9166 (ttmt) cc_final: 0.8872 (mttt)
REVERT: H  130 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7635 (tm-30)
  outliers start: 14
  outliers final: 10
  residues processed: 164
  average time/residue: 0.3809
  time to fit residues: 78.2826
Evaluate side-chains
  170 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 157
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue   18 ARG
Chi-restraints excluded: chain C residue   65 GLU
Chi-restraints excluded: chain C residue  109 MET
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain G residue   39 LYS
Chi-restraints excluded: chain G residue  102 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 93 optimal weight:   10.0000
   chunk 88 optimal weight:    6.9990
   chunk 77 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 75 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.110867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.074276 restraints weight = 20683.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.2911 rms_B_bonded: 1.63
r_work: 0.2727 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8703
moved from start:          0.6007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11921  Z= 0.190
  Angle     :  0.559   7.320  17247  Z= 0.331
  Chirality :  0.035   0.235   1972
  Planarity :  0.004   0.035   1249
  Dihedral  : 30.227 178.318   3713
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 15.44 %
    Favored  : 82.55 %
  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:  2.29 (0.33), residues: 707
  helix:  2.48 (0.23), residues: 520
  sheet:  None (None), residues: 0
  loop : -1.41 (0.41), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D  74 
 PHE   0.015   0.001   PHE C  26 
 TYR   0.008   0.001   TYR B  51 
 ARG   0.003   0.000   ARG D 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05042 (  575)
  hydrogen bonds       : angle       2.67455 ( 1488)
  covalent geometry    : bond        0.00434 (11921)
  covalent geometry    : angle       0.55883 (17247)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 158
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.8962 (tttm) cc_final: 0.8741 (tttt)
REVERT: C   18 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8219 (mpp80)
REVERT: C   73 ASP cc_start: 0.8480 (m-30) cc_final: 0.8231 (m-30)
REVERT: C   74 ASN cc_start: 0.8084 (m-40) cc_final: 0.7655 (t0)
REVERT: C  105 ASN cc_start: 0.9049 (t0) cc_final: 0.8207 (t0)
REVERT: C  109 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8119 (mtm)
REVERT: D  104 LYS cc_start: 0.8178 (mptt) cc_final: 0.7923 (mtmm)
REVERT: D  111 LYS cc_start: 0.8688 (mmtm) cc_final: 0.8268 (mtpt)
REVERT: F   79 LYS cc_start: 0.9110 (mtpt) cc_final: 0.8880 (mtmm)
REVERT: H   63 LYS cc_start: 0.9024 (mptt) cc_final: 0.8781 (mmtp)
REVERT: H   68 LYS cc_start: 0.9180 (ttmt) cc_final: 0.8887 (mttt)
REVERT: H  130 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7659 (tm-30)
  outliers start: 12
  outliers final: 9
  residues processed: 161
  average time/residue: 0.3760
  time to fit residues: 75.6013
Evaluate side-chains
  164 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 153
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue   18 ARG
Chi-restraints excluded: chain C residue   65 GLU
Chi-restraints excluded: chain C residue  109 MET
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain G residue   39 LYS
Chi-restraints excluded: chain G residue  102 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 50 optimal weight:    0.0060
   chunk 22 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 72 optimal weight:    5.9990
   chunk 25 optimal weight:    0.5980
   chunk 41 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 92 optimal weight:    8.9990
   overall best weight:    1.1200

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.111448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.075347 restraints weight = 20528.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.2937 rms_B_bonded: 1.46
r_work: 0.2760 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2610 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8840
moved from start:          0.6032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11921  Z= 0.161
  Angle     :  0.549   7.168  17247  Z= 0.326
  Chirality :  0.034   0.172   1972
  Planarity :  0.004   0.035   1249
  Dihedral  : 30.223 178.395   3713
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 15.44 %
    Favored  : 82.55 %
  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:  2.34 (0.33), residues: 707
  helix:  2.52 (0.23), residues: 521
  sheet:  None (None), residues: 0
  loop : -1.44 (0.42), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B  75 
 PHE   0.014   0.001   PHE C  26 
 TYR   0.008   0.001   TYR B  51 
 ARG   0.003   0.000   ARG C  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04816 (  575)
  hydrogen bonds       : angle       2.65218 ( 1488)
  covalent geometry    : bond        0.00355 (11921)
  covalent geometry    : angle       0.54862 (17247)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 153
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
REVERT: C   18 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8278 (mpp80)
REVERT: C   73 ASP cc_start: 0.8596 (m-30) cc_final: 0.8364 (m-30)
REVERT: C   74 ASN cc_start: 0.8156 (m-40) cc_final: 0.7720 (t0)
REVERT: C  105 ASN cc_start: 0.9095 (t0) cc_final: 0.8273 (t0)
REVERT: C  109 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8340 (mtm)
REVERT: D  104 LYS cc_start: 0.8379 (mptt) cc_final: 0.8149 (mtmm)
REVERT: D  111 LYS cc_start: 0.8744 (mmtm) cc_final: 0.8383 (mtpt)
REVERT: H   63 LYS cc_start: 0.9050 (mptt) cc_final: 0.8843 (mmtp)
REVERT: H   68 LYS cc_start: 0.9208 (ttmt) cc_final: 0.8941 (mttt)
REVERT: H  130 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7895 (tm-30)
  outliers start: 12
  outliers final: 10
  residues processed: 156
  average time/residue: 0.3909
  time to fit residues: 76.4129
Evaluate side-chains
  163 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 151
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue   18 ARG
Chi-restraints excluded: chain C residue   65 GLU
Chi-restraints excluded: chain C residue  109 MET
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain G residue   39 LYS
Chi-restraints excluded: chain G residue  102 THR
Chi-restraints excluded: chain H residue   64 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 45 optimal weight:    0.5980
   chunk 19 optimal weight:    4.9990
   chunk 80 optimal weight:   10.0000
   chunk 66 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 52 optimal weight:    0.5980
   chunk 72 optimal weight:    5.9990
   chunk 28 optimal weight:    0.7980
   chunk 70 optimal weight:    8.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
F  25 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.111535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.075064 restraints weight = 20589.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.2927 rms_B_bonded: 1.63
r_work: 0.2743 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8688
moved from start:          0.6039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11921  Z= 0.160
  Angle     :  0.546   7.153  17247  Z= 0.324
  Chirality :  0.034   0.168   1972
  Planarity :  0.004   0.035   1249
  Dihedral  : 30.207 178.362   3713
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.77 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.34 (0.33), residues: 707
  helix:  2.52 (0.23), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.45 (0.42), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B  75 
 PHE   0.012   0.001   PHE C  26 
 TYR   0.008   0.001   TYR H  65 
 ARG   0.003   0.000   ARG C  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04731 (  575)
  hydrogen bonds       : angle       2.63206 ( 1488)
  covalent geometry    : bond        0.00352 (11921)
  covalent geometry    : angle       0.54604 (17247)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 149
  time to evaluate  : 0.826 
Fit side-chains
   revert: symmetry clash
REVERT: C   18 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8263 (mpp80)
REVERT: C   73 ASP cc_start: 0.8471 (m-30) cc_final: 0.8223 (m-30)
REVERT: C   74 ASN cc_start: 0.8041 (m-40) cc_final: 0.7616 (t0)
REVERT: C  105 ASN cc_start: 0.9044 (t0) cc_final: 0.8187 (t0)
REVERT: C  109 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8103 (mtm)
REVERT: D  104 LYS cc_start: 0.8169 (mptt) cc_final: 0.7925 (mtmm)
REVERT: D  111 LYS cc_start: 0.8673 (mmtm) cc_final: 0.8267 (mtpt)
REVERT: H   63 LYS cc_start: 0.9028 (mptt) cc_final: 0.8782 (mmtp)
REVERT: H   68 LYS cc_start: 0.9177 (ttmt) cc_final: 0.8891 (mttt)
REVERT: H  130 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7629 (tm-30)
  outliers start: 13
  outliers final: 10
  residues processed: 153
  average time/residue: 0.3722
  time to fit residues: 71.4975
Evaluate side-chains
  161 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 149
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue   18 ARG
Chi-restraints excluded: chain C residue   65 GLU
Chi-restraints excluded: chain C residue  109 MET
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain G residue   39 LYS
Chi-restraints excluded: chain G residue  102 THR
Chi-restraints excluded: chain H residue   64 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 16 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 88 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9990
   chunk 86 optimal weight:    4.9990
   chunk 85 optimal weight:    5.9990
   chunk 20 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   chunk 60 optimal weight:    3.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.111922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.075916 restraints weight = 20449.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.2948 rms_B_bonded: 1.47
r_work: 0.2775 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2624 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8814
moved from start:          0.6056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11921  Z= 0.153
  Angle     :  0.545   7.168  17247  Z= 0.323
  Chirality :  0.034   0.158   1972
  Planarity :  0.004   0.035   1249
  Dihedral  : 30.197 178.403   3713
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.77 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.39 (0.33), residues: 707
  helix:  2.57 (0.23), residues: 521
  sheet:  None (None), residues: 0
  loop : -1.44 (0.42), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B  75 
 PHE   0.011   0.001   PHE C  26 
 TYR   0.008   0.001   TYR H  65 
 ARG   0.003   0.000   ARG C  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04622 (  575)
  hydrogen bonds       : angle       2.62570 ( 1488)
  covalent geometry    : bond        0.00332 (11921)
  covalent geometry    : angle       0.54481 (17247)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5624.77 seconds
wall clock time: 97 minutes 36.37 seconds (5856.37 seconds total)