Starting phenix.real_space_refine
on Fri Mar  6 05:00:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7oi0_12916/03_2026/7oi0_12916.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7oi0_12916/03_2026/7oi0_12916.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7oi0_12916/03_2026/7oi0_12916.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7oi0_12916/03_2026/7oi0_12916.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7oi0_12916/03_2026/7oi0_12916.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7oi0_12916/03_2026/7oi0_12916.map"
  }
  resolution = 2.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.007 sd=   0.083
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     963      5.49       5
     S      30      5.16       5
     C   14335      2.51       5
     N    5400      2.21       5
     O    8527      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 29255
  Number of models: 1
  Model: ""
    Number of chains: 17
    Chain: "D"
      Number of atoms: 1643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 205, 1643
          Classifications: {'peptide': 205}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 198}
    Chain: "F"
      Number of atoms: 817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 817
          Classifications: {'peptide': 100}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
    Chain: "H"
      Number of atoms: 979
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 979
          Classifications: {'peptide': 129}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 123}
    Chain: "K"
      Number of atoms: 702
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 702
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "L"
      Number of atoms: 955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 955
          Classifications: {'peptide': 123}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 115}
    Chain: "O"
      Number of atoms: 716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 716
          Classifications: {'peptide': 88}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 87}
    Chain: "P"
      Number of atoms: 649
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 649
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 79}
    Chain: "Q"
      Number of atoms: 648
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 648
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 2, 'TRANS': 77}
    Chain: "R"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 407
          Classifications: {'peptide': 50}
          Link IDs: {'PTRANS': 2, 'TRANS': 47}
    Chain: "T"
      Number of atoms: 665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 665
          Classifications: {'peptide': 85}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 83}
    Chain: "A"
      Number of atoms: 20700
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 963, 20700
          Classifications: {'RNA': 963}
          Modifications used: {'rna2p_pur': 74, 'rna2p_pyr': 44, 'rna3p_pur': 487, 'rna3p_pyr': 358}
          Link IDs: {'rna2p': 118, 'rna3p': 844}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Classifications: {'water': 6}
          Link IDs: {None: 5}
    Chain: "L"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "P"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 18
          Classifications: {'water': 18}
          Link IDs: {None: 17}
    Chain: "Q"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "T"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Classifications: {'water': 6}
          Link IDs: {None: 5}
    Chain: "A"
      Number of atoms: 337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 337
          Classifications: {'water': 337}
          Link IDs: {None: 336}
  Time building chain proxies: 5.78, per 1000 atoms: 0.20
  Number of scatterers: 29255
  At special positions: 0
  Unit cell: (111.8, 155.66, 212.42, 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      30     16.00
     P     963     15.00
     O    8527      8.00
     N    5400      7.00
     C   14335      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: 2.27
  Conformation dependent library (CDL) restraints added in 629.2 milliseconds
  

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1930

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 11 sheets defined
      39.9% alpha, 15.9% beta
      338 base pairs and 532 stacking pairs defined.
    Time for finding SS restraints: 4.85
  Creating SS restraints...
    Processing helix  chain 'D' and resid 6 through 14
      removed outlier: 3.928A  pdb=" N   LEU D  10 " --> pdb=" O   PRO D   6 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   SER D  11 " --> pdb=" O   LYS D   7 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   GLU D  14 " --> pdb=" O   LEU D  10 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 48 through 65
    Processing helix  chain 'D' and resid 67 through 81
    Processing helix  chain 'D' and resid 84 through 95
    Processing helix  chain 'D' and resid 96 through 104
    Processing helix  chain 'D' and resid 109 through 119
    Processing helix  chain 'D' and resid 146 through 149
    Processing helix  chain 'D' and resid 151 through 160
      removed outlier: 3.603A  pdb=" N   GLU D 159 " --> pdb=" O   LYS D 155 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU D 160 " --> pdb=" O   ALA D 156 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 195 through 203
      removed outlier: 4.030A  pdb=" N   ILE D 199 " --> pdb=" O   ASN D 195 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 14 through 16
      No H-bonds generated for 'chain 'F' and resid 14 through 16'
    Processing helix  chain 'F' and resid 17 through 32
    Processing helix  chain 'F' and resid 50 through 54
      removed outlier: 3.640A  pdb=" N   LYS F  53 " --> pdb=" O   PRO F  50 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU F  54 " --> pdb=" O   ILE F  51 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 50 through 54'
    Processing helix  chain 'F' and resid 69 through 81
      removed outlier: 4.153A  pdb=" N   GLU F  73 " --> pdb=" O   GLU F  69 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   LEU F  74 " --> pdb=" O   VAL F  70 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 4 through 19
      removed outlier: 3.694A  pdb=" N   MET H   9 " --> pdb=" O   PRO H   5 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 29 through 42
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'H' and resid 111 through 119
    Processing helix  chain 'K' and resid 58 through 72
    Processing helix  chain 'K' and resid 91 through 101
    Processing helix  chain 'L' and resid 2 through 9
    Processing helix  chain 'O' and resid 3 through 14
    Processing helix  chain 'O' and resid 23 through 46
      removed outlier: 4.111A  pdb=" N   ALA O  43 " --> pdb=" O   GLN O  39 " (cutoff:3.500A)
      removed outlier: 5.275A  pdb=" N   GLU O  44 " --> pdb=" O   GLY O  40 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   HIS O  45 " --> pdb=" O   HIS O  41 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 49 through 73
      removed outlier: 3.678A  pdb=" N   ARG O  53 " --> pdb=" O   HIS O  49 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   GLY O  54 " --> pdb=" O   HIS O  50 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU O  55 " --> pdb=" O   SER O  51 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 73 through 84
      removed outlier: 5.012A  pdb=" N   GLU O  82 " --> pdb=" O   THR O  78 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 53 through 63
      removed outlier: 3.845A  pdb=" N   ILE P  57 " --> pdb=" O   ASP P  53 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 68 through 82
    Processing helix  chain 'R' and resid 25 through 32
      removed outlier: 3.662A  pdb=" N   LYS R  29 " --> pdb=" O   ALA R  26 " (cutoff:3.500A)
      removed outlier: 5.355A  pdb=" N   ASN R  30 " --> pdb=" O   THR R  27 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 49 through 64
    Processing helix  chain 'T' and resid 3 through 39
    Processing helix  chain 'T' and resid 42 through 63
      Proline residue:  T  55  - end of helix
    Processing helix  chain 'T' and resid 67 through 86
    Processing sheet with id=AA1, first strand: chain 'D' and resid 127 through 128
    Processing sheet with id=AA2, first strand: chain 'F' and resid 2 through 3
    Processing sheet with id=AA3, first strand: chain 'F' and resid 40 through 46
      removed outlier: 3.736A  pdb=" N   GLU F  40 " --> pdb=" O   LEU F  61 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU F  61 " --> pdb=" O   GLU F  40 " (cutoff:3.500A)
      removed outlier: 5.233A  pdb=" N   TYR F  59 " --> pdb=" O   TRP F  42 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   ARG F  44 " --> pdb=" O   ALA F  57 " (cutoff:3.500A)
      removed outlier: 4.987A  pdb=" N   ALA F  57 " --> pdb=" O   ARG F  44 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 23 through 24
    Processing sheet with id=AA5, first strand: chain 'H' and resid 50 through 51
    Processing sheet with id=AA6, first strand: chain 'H' and resid 75 through 76
    Processing sheet with id=AA7, first strand: chain 'H' and resid 75 through 76
      removed outlier: 6.900A  pdb=" N   VAL H 102 " --> pdb=" O   ILE H 125 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'K' and resid 40 through 45
      removed outlier: 6.645A  pdb=" N   ILE K  33 " --> pdb=" O   LEU K  41 " (cutoff:3.500A)
      removed outlier: 5.036A  pdb=" N   TRP K  43 " --> pdb=" O   VAL K  31 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   VAL K  31 " --> pdb=" O   TRP K  43 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 28 through 31
      removed outlier: 10.174A  pdb=" N   VAL L  92 " --> pdb=" O   GLU L  61 " (cutoff:3.500A)
      removed outlier: 8.037A  pdb=" N   THR L  63 " --> pdb=" O   VAL L  92 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   TYR L  94 " --> pdb=" O   THR L  63 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'P' and resid 50 through 51
      removed outlier: 4.865A  pdb=" N   VAL P  19 " --> pdb=" O   VAL P  36 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   PHE P  38 " --> pdb=" O   TYR P  17 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   TYR P  17 " --> pdb=" O   PHE P  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'Q' and resid 7 through 16
      removed outlier: 7.901A  pdb=" N   GLN Q   8 " --> pdb=" O   GLU Q  25 " (cutoff:3.500A)
      removed outlier: 5.223A  pdb=" N   GLU Q  25 " --> pdb=" O   GLN Q   8 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   VAL Q  21 " --> pdb=" O   VAL Q  12 " (cutoff:3.500A)
      removed outlier: 4.965A  pdb=" N   ASP Q  14 " --> pdb=" O   SER Q  19 " (cutoff:3.500A)
      removed outlier: 7.447A  pdb=" N   SER Q  19 " --> pdb=" O   ASP Q  14 " (cutoff:3.500A)
      removed outlier: 15.667A  pdb=" N   LYS Q  70 " --> pdb=" O   THR Q  40 " (cutoff:3.500A)
      removed outlier: 14.072A  pdb=" N   LYS Q  42 " --> pdb=" O   LYS Q  70 " (cutoff:3.500A)
      removed outlier: 9.785A  pdb=" N   TRP Q  72 " --> pdb=" O   LYS Q  42 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   HIS Q  44 " --> pdb=" O   TRP Q  72 " (cutoff:3.500A)
      removed outlier: 7.683A  pdb=" N   LEU Q  74 " --> pdb=" O   HIS Q  44 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   HIS Q  46 " --> pdb=" O   LEU Q  74 " (cutoff:3.500A)
      removed outlier: 8.720A  pdb=" N   ARG Q  76 " --> pdb=" O   HIS Q  46 " (cutoff:3.500A)
      removed outlier: 5.922A  pdb=" N   SER Q  71 " --> pdb=" O   CYS Q  63 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   GLU Q  59 " --> pdb=" O   VAL Q  75 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   VAL Q  77 " --> pdb=" O   VAL Q  57 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   VAL Q  57 " --> pdb=" O   VAL Q  77 " (cutoff:3.500A)

    363 hydrogen bonds defined for protein.
    1023 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      840 hydrogen bonds
      1286 hydrogen bond angles
      0 basepair planarities
      338 basepair parallelities
      532 stacking parallelities
  Total time for adding SS restraints: 11.42

  Time building geometry restraints manager: 3.23 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 2788
        1.30 -     1.43: 14063
        1.43 -     1.56: 12652
        1.56 -     1.68: 1924
        1.68 -     1.81: 51
  Bond restraints: 31478
  Sorted by residual:
  bond pdb=" CB  VAL P  20 "
       pdb=" CG2 VAL P  20 "
    ideal  model  delta    sigma   weight residual
    1.521  1.404  0.117 3.30e-02 9.18e+02 1.25e+01
  bond pdb=" C5    G A 108 "
       pdb=" C6    G A 108 "
    ideal  model  delta    sigma   weight residual
    1.419  1.350  0.069 2.00e-02 2.50e+03 1.20e+01
  bond pdb=" N   ILE T  66 "
       pdb=" CA  ILE T  66 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.036 1.11e-02 8.12e+03 1.03e+01
  bond pdb=" N9    A A 452 "
       pdb=" C4    A A 452 "
    ideal  model  delta    sigma   weight residual
    1.374  1.310  0.064 2.00e-02 2.50e+03 1.02e+01
  bond pdb=" CD2 HIS P   9 "
       pdb=" NE2 HIS P   9 "
    ideal  model  delta    sigma   weight residual
    1.374  1.339  0.035 1.10e-02 8.26e+03 9.97e+00
  ... (remaining 31473 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.52: 45535
        2.52 -     5.04: 1588
        5.04 -     7.57: 149
        7.57 -    10.09: 17
       10.09 -    12.61: 7
  Bond angle restraints: 47296
  Sorted by residual:
  angle pdb=" C4'   G A 416 "
        pdb=" C3'   G A 416 "
        pdb=" O3'   G A 416 "
      ideal   model   delta    sigma   weight residual
     113.00  125.61  -12.61 1.50e+00 4.44e-01 7.07e+01
  angle pdb=" O2'   G A 416 "
        pdb=" C2'   G A 416 "
        pdb=" C1'   G A 416 "
      ideal   model   delta    sigma   weight residual
     108.40   97.74   10.66 1.50e+00 4.44e-01 5.05e+01
  angle pdb=" C4'   A A 465 "
        pdb=" C3'   A A 465 "
        pdb=" O3'   A A 465 "
      ideal   model   delta    sigma   weight residual
     113.00  123.41  -10.41 1.50e+00 4.44e-01 4.82e+01
  angle pdb=" C4'   A A 415 "
        pdb=" C3'   A A 415 "
        pdb=" O3'   A A 415 "
      ideal   model   delta    sigma   weight residual
     113.00  121.46   -8.46 1.50e+00 4.44e-01 3.18e+01
  angle pdb=" O4'   A A 182 "
        pdb=" C1'   A A 182 "
        pdb=" N9    A A 182 "
      ideal   model   delta    sigma   weight residual
     108.20  116.16   -7.96 1.50e+00 4.44e-01 2.82e+01
  ... (remaining 47291 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.35: 17480
       35.35 -    70.70: 2452
       70.70 -   106.05: 275
      106.05 -   141.39: 7
      141.39 -   176.74: 11
  Dihedral angle restraints: 20225
    sinusoidal: 17239
      harmonic: 2986
  Sorted by residual:
  dihedral pdb=" O4'   U A 610 "
           pdb=" C1'   U A 610 "
           pdb=" N1    U A 610 "
           pdb=" C2    U A 610 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00    5.95 -165.95     1      1.50e+01 4.44e-03 8.41e+01
  dihedral pdb=" O4'   U A 365 "
           pdb=" C1'   U A 365 "
           pdb=" N1    U A 365 "
           pdb=" C2    U A 365 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   50.60  149.40     1      1.50e+01 4.44e-03 7.94e+01
  dihedral pdb=" O4'   C A 754 "
           pdb=" C1'   C A 754 "
           pdb=" N1    C A 754 "
           pdb=" C2    C A 754 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   50.65  149.35     1      1.50e+01 4.44e-03 7.94e+01
  ... (remaining 20222 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.138: 5788
       0.138 -    0.275: 254
       0.275 -    0.413: 13
       0.413 -    0.551: 0
       0.551 -    0.689: 1
  Chirality restraints: 6056
  Sorted by residual:
  chirality pdb=" C3'   A A 465 "
            pdb=" C4'   A A 465 "
            pdb=" O3'   A A 465 "
            pdb=" C2'   A A 465 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -1.79   -0.69 2.00e-01 2.50e+01 1.19e+01
  chirality pdb=" CB  VAL P  20 "
            pdb=" CA  VAL P  20 "
            pdb=" CG1 VAL P  20 "
            pdb=" CG2 VAL P  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.24   -0.39 2.00e-01 2.50e+01 3.79e+00
  chirality pdb=" CB  ILE L  66 "
            pdb=" CA  ILE L  66 "
            pdb=" CG1 ILE L  66 "
            pdb=" CG2 ILE L  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.27    0.37 2.00e-01 2.50e+01 3.44e+00
  ... (remaining 6053 not shown)

  Planarity restraints: 2401
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C A 335 "   -0.069 2.00e-02 2.50e+03   3.65e-02 3.00e+01
        pdb=" N1    C A 335 "    0.080 2.00e-02 2.50e+03
        pdb=" C2    C A 335 "    0.002 2.00e-02 2.50e+03
        pdb=" O2    C A 335 "    0.008 2.00e-02 2.50e+03
        pdb=" N3    C A 335 "   -0.008 2.00e-02 2.50e+03
        pdb=" C4    C A 335 "   -0.005 2.00e-02 2.50e+03
        pdb=" N4    C A 335 "   -0.018 2.00e-02 2.50e+03
        pdb=" C5    C A 335 "   -0.006 2.00e-02 2.50e+03
        pdb=" C6    C A 335 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A A 181 "   -0.069 2.00e-02 2.50e+03   3.16e-02 2.75e+01
        pdb=" N9    A A 181 "    0.072 2.00e-02 2.50e+03
        pdb=" C8    A A 181 "    0.012 2.00e-02 2.50e+03
        pdb=" N7    A A 181 "   -0.013 2.00e-02 2.50e+03
        pdb=" C5    A A 181 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    A A 181 "   -0.011 2.00e-02 2.50e+03
        pdb=" N6    A A 181 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1    A A 181 "   -0.014 2.00e-02 2.50e+03
        pdb=" C2    A A 181 "    0.009 2.00e-02 2.50e+03
        pdb=" N3    A A 181 "    0.009 2.00e-02 2.50e+03
        pdb=" C4    A A 181 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U A 438 "    0.064 2.00e-02 2.50e+03   3.21e-02 2.32e+01
        pdb=" N1    U A 438 "   -0.063 2.00e-02 2.50e+03
        pdb=" C2    U A 438 "   -0.014 2.00e-02 2.50e+03
        pdb=" O2    U A 438 "   -0.009 2.00e-02 2.50e+03
        pdb=" N3    U A 438 "    0.015 2.00e-02 2.50e+03
        pdb=" C4    U A 438 "    0.008 2.00e-02 2.50e+03
        pdb=" O4    U A 438 "    0.014 2.00e-02 2.50e+03
        pdb=" C5    U A 438 "    0.004 2.00e-02 2.50e+03
        pdb=" C6    U A 438 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 2398 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 729
        2.56 -     3.15: 23322
        3.15 -     3.73: 63512
        3.73 -     4.32: 87681
        4.32 -     4.90: 112427
  Nonbonded interactions: 287671
  Sorted by model distance:
  nonbonded pdb=" N2    G A 444 "
            pdb=" O2    C A 490 "
     model   vdw
     1.977 2.496
  nonbonded pdb=" N2    G A 457 "
            pdb=" O2    C A 475 "
     model   vdw
     1.982 2.496
  nonbonded pdb=" O6    G A 410 "
            pdb=" O2'   U A 429 "
     model   vdw
     1.983 3.040
  nonbonded pdb=" O2    C A 658 "
            pdb=" N2    G A 748 "
     model   vdw
     2.021 2.496
  nonbonded pdb=" OD1 ASP D  98 "
            pdb=" N   ASN D  99 "
     model   vdw
     2.025 3.120
  ... (remaining 287666 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             5.620
  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:             0.030
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.090
  Set scattering table:                    0.090
  Process input model:                     33.700
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  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:             0.020
  Load rotamer database and sin/cos tables:8.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7270
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      :  0.014   0.117  31478  Z= 0.729
  Angle     :  1.079  12.609  47296  Z= 0.566
  Chirality :  0.063   0.689   6056
  Planarity :  0.007   0.062   2401
  Dihedral  : 24.491 176.743  18295
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 23.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.23 %
    Favored  : 89.77 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.23 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.50 (0.24), residues: 1017
  helix: -0.71 (0.26), residues: 379
  sheet: -2.44 (0.38), residues: 147
  loop : -2.14 (0.26), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.002   ARG P  14 
 TYR   0.027   0.003   TYR L 116 
 PHE   0.016   0.003   PHE P  39 
 TRP   0.016   0.002   TRP Q  72 
 HIS   0.013   0.002   HIS D 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.01402 (31478)
  covalent geometry    : angle       1.07882 (47296)
  hydrogen bonds       : bond        0.16612 ( 1201)
  hydrogen bonds       : angle       5.63530 ( 2309)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 113
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 3
  residues processed: 115
  average time/residue: 0.7663
  time to fit residues: 102.1519
Evaluate side-chains
  105 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 102
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    8 LEU
Chi-restraints excluded: chain L residue   19 ASN
Chi-restraints excluded: chain O residue   67 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 194 optimal weight:   30.0000
   chunk 107 optimal weight:   20.0000
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    0.6980
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    0.5980
   chunk 91 optimal weight:   20.0000
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F   3 HIS
** F  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 100 ASN
L   4 ASN
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  95 HIS
** O  45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.157491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.132492 restraints weight = 50406.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.4072 rms_B_bonded: 0.46
r_work: 0.3710 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3638 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.2054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  31478  Z= 0.146
  Angle     :  0.647  10.306  47296  Z= 0.330
  Chirality :  0.036   0.242   6056
  Planarity :  0.005   0.054   2401
  Dihedral  : 24.660 176.837  16234
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 10.84 %
    Favored  : 87.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.47 (0.25), residues: 1017
  helix:  0.59 (0.26), residues: 385
  sheet: -2.09 (0.38), residues: 159
  loop : -1.91 (0.27), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG T  28 
 TYR   0.013   0.002   TYR F  59 
 PHE   0.009   0.001   PHE D 106 
 TRP   0.006   0.001   TRP P  60 
 HIS   0.009   0.001   HIS O  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (31478)
  covalent geometry    : angle       0.64691 (47296)
  hydrogen bonds       : bond        0.09112 ( 1201)
  hydrogen bonds       : angle       3.64841 ( 2309)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 117
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    9 MET cc_start: -0.2461 (pmt) cc_final: -0.2899 (pmm)
REVERT: Q   59 GLU cc_start: 0.7312 (mt-10) cc_final: 0.7061 (mt-10)
  outliers start: 11
  outliers final: 2
  residues processed: 124
  average time/residue: 0.7688
  time to fit residues: 110.2465
Evaluate side-chains
  101 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue    3 HIS
Chi-restraints excluded: chain L residue   63 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 183 optimal weight:   30.0000
   chunk 179 optimal weight:   50.0000
   chunk 192 optimal weight:   50.0000
   chunk 103 optimal weight:    3.9990
   chunk 165 optimal weight:   10.0000
   chunk 149 optimal weight:    4.9990
   chunk 180 optimal weight:   10.0000
   chunk 18 optimal weight:    9.9990
   chunk 166 optimal weight:   30.0000
   chunk 82 optimal weight:    0.9990
   chunk 23 optimal weight:    6.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
D 151 GLN
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  95 HIS
** O  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.151764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.124007 restraints weight = 49525.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3939 rms_B_bonded: 1.10
r_work: 0.3571 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3517 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.1437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.075  31478  Z= 0.567
  Angle     :  0.895  11.008  47296  Z= 0.440
  Chirality :  0.051   0.381   6056
  Planarity :  0.007   0.077   2401
  Dihedral  : 24.747 178.583  16228
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 13.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.57 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 13.29 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.58 (0.25), residues: 1017
  helix:  0.40 (0.25), residues: 386
  sheet: -2.23 (0.39), residues: 158
  loop : -1.84 (0.27), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG Q  76 
 TYR   0.025   0.003   TYR L 116 
 PHE   0.016   0.002   PHE D 106 
 TRP   0.014   0.002   TRP Q  72 
 HIS   0.018   0.002   HIS O  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.01109 (31478)
  covalent geometry    : angle       0.89481 (47296)
  hydrogen bonds       : bond        0.11783 ( 1201)
  hydrogen bonds       : angle       3.76721 ( 2309)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 97
  time to evaluate  : 0.578 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    9 MET cc_start: -0.2169 (pmt) cc_final: -0.2731 (pmm)
REVERT: H   79 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8212 (ptm-80)
REVERT: L  107 LYS cc_start: 0.7391 (mppt) cc_final: 0.7133 (mppt)
  outliers start: 28
  outliers final: 7
  residues processed: 116
  average time/residue: 0.7464
  time to fit residues: 100.5250
Evaluate side-chains
  101 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   60 LEU
Chi-restraints excluded: chain H residue   79 ARG
Chi-restraints excluded: chain H residue   82 LEU
Chi-restraints excluded: chain H residue   84 ILE
Chi-restraints excluded: chain L residue   63 THR
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue  118 VAL
Chi-restraints excluded: chain T residue   85 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 22 optimal weight:    6.9990
   chunk 16 optimal weight:    8.9990
   chunk 80 optimal weight:    3.9990
   chunk 135 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 149 optimal weight:    0.5980
   chunk 141 optimal weight:    6.9990
   chunk 156 optimal weight:    6.9990
   chunk 120 optimal weight:   10.0000
   chunk 3 optimal weight:    6.9990
   chunk 133 optimal weight:    2.9990
   overall best weight:    1.8386

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

Flipped N/Q/H residues before XYZ refinement:
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F   3 HIS
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  95 HIS
** O  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  44 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.154741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.127726 restraints weight = 49620.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3998 rms_B_bonded: 0.72
r_work: 0.3633 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3580 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.2174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  31478  Z= 0.230
  Angle     :  0.649  13.187  47296  Z= 0.328
  Chirality :  0.037   0.257   6056
  Planarity :  0.005   0.048   2401
  Dihedral  : 24.501 179.926  16228
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 15.50 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.26 (0.26), residues: 1017
  helix:  0.84 (0.26), residues: 386
  sheet: -2.31 (0.40), residues: 153
  loop : -1.73 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H 116 
 TYR   0.016   0.002   TYR D  75 
 PHE   0.013   0.001   PHE P  32 
 TRP   0.007   0.001   TRP Q  72 
 HIS   0.009   0.001   HIS O  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 (31478)
  covalent geometry    : angle       0.64882 (47296)
  hydrogen bonds       : bond        0.09134 ( 1201)
  hydrogen bonds       : angle       3.38431 ( 2309)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 105
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   20 LEU cc_start: 0.6420 (OUTLIER) cc_final: 0.6205 (pp)
REVERT: H  110 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.7127 (pmm)
  outliers start: 27
  outliers final: 9
  residues processed: 121
  average time/residue: 0.7577
  time to fit residues: 106.4561
Evaluate side-chains
  107 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   20 LEU
Chi-restraints excluded: chain F residue    3 HIS
Chi-restraints excluded: chain H residue   60 LEU
Chi-restraints excluded: chain H residue   84 ILE
Chi-restraints excluded: chain H residue  110 MET
Chi-restraints excluded: chain L residue   19 ASN
Chi-restraints excluded: chain L residue   38 THR
Chi-restraints excluded: chain L residue   63 THR
Chi-restraints excluded: chain L residue  118 VAL
Chi-restraints excluded: chain P residue   20 VAL
Chi-restraints excluded: chain T residue   85 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 172 optimal weight:   10.0000
   chunk 170 optimal weight:   50.0000
   chunk 131 optimal weight:    2.9990
   chunk 106 optimal weight:    4.9990
   chunk 148 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   chunk 171 optimal weight:   30.0000
   chunk 179 optimal weight:   50.0000
   chunk 7 optimal weight:    0.7980
   chunk 89 optimal weight:    9.9990
   overall best weight:    2.1584

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

Flipped N/Q/H residues before XYZ refinement:
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F   3 HIS
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
O  41 HIS
** Q   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.154315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.127988 restraints weight = 49522.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.4003 rms_B_bonded: 0.78
r_work: 0.3642 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3579 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.2309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  31478  Z= 0.259
  Angle     :  0.664  11.042  47296  Z= 0.334
  Chirality :  0.038   0.258   6056
  Planarity :  0.005   0.040   2401
  Dihedral  : 24.428 178.674  16228
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 15.85 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.13 (0.26), residues: 1017
  helix:  0.94 (0.26), residues: 388
  sheet: -2.27 (0.39), residues: 154
  loop : -1.65 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG H 116 
 TYR   0.016   0.002   TYR F   4 
 PHE   0.011   0.001   PHE P  32 
 TRP   0.008   0.001   TRP Q  72 
 HIS   0.016   0.002   HIS F   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 (31478)
  covalent geometry    : angle       0.66368 (47296)
  hydrogen bonds       : bond        0.09331 ( 1201)
  hydrogen bonds       : angle       3.33966 ( 2309)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 100
  time to evaluate  : 0.655 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    9 MET cc_start: -0.2258 (pmt) cc_final: -0.2689 (pmm)
REVERT: H  110 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.7210 (pmm)
REVERT: P    5 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.7850 (ptp-170)
  outliers start: 30
  outliers final: 12
  residues processed: 122
  average time/residue: 0.7189
  time to fit residues: 102.0997
Evaluate side-chains
  111 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  106 PHE
Chi-restraints excluded: chain F residue   23 GLU
Chi-restraints excluded: chain H residue   60 LEU
Chi-restraints excluded: chain H residue   84 ILE
Chi-restraints excluded: chain H residue  110 MET
Chi-restraints excluded: chain L residue   19 ASN
Chi-restraints excluded: chain L residue   38 THR
Chi-restraints excluded: chain L residue   63 THR
Chi-restraints excluded: chain L residue   66 ILE
Chi-restraints excluded: chain L residue  118 VAL
Chi-restraints excluded: chain P residue    5 ARG
Chi-restraints excluded: chain P residue   20 VAL
Chi-restraints excluded: chain Q residue   66 LEU
Chi-restraints excluded: chain T residue   85 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 168 optimal weight:   50.0000
   chunk 64 optimal weight:    7.9990
   chunk 94 optimal weight:    0.6980
   chunk 43 optimal weight:    5.9990
   chunk 23 optimal weight:   10.0000
   chunk 178 optimal weight:   50.0000
   chunk 180 optimal weight:   10.0000
   chunk 121 optimal weight:    3.9990
   chunk 139 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 21 optimal weight:    9.9990
   overall best weight:    3.1388

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

Flipped N/Q/H residues before XYZ refinement:
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  95 HIS
** Q   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
T  12 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.153127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.127081 restraints weight = 49278.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3991 rms_B_bonded: 0.90
r_work: 0.3628 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3572 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.051  31478  Z= 0.351
  Angle     :  0.729  12.340  47296  Z= 0.364
  Chirality :  0.041   0.283   6056
  Planarity :  0.005   0.053   2401
  Dihedral  : 24.476 178.654  16228
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 17.72 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.16 (0.26), residues: 1017
  helix:  0.85 (0.26), residues: 388
  sheet: -2.26 (0.41), residues: 149
  loop : -1.63 (0.27), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG H 116 
 TYR   0.019   0.002   TYR D  75 
 PHE   0.011   0.001   PHE P  32 
 TRP   0.011   0.001   TRP Q  72 
 HIS   0.006   0.001   HIS K  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00680 (31478)
  covalent geometry    : angle       0.72856 (47296)
  hydrogen bonds       : bond        0.10022 ( 1201)
  hydrogen bonds       : angle       3.39372 ( 2309)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 101
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   67 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8619 (mp)
REVERT: F    9 MET cc_start: -0.2256 (pmt) cc_final: -0.2739 (pmm)
REVERT: H   79 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8218 (ptm-80)
  outliers start: 27
  outliers final: 16
  residues processed: 118
  average time/residue: 0.7006
  time to fit residues: 96.4174
Evaluate side-chains
  115 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  106 PHE
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain F residue   23 GLU
Chi-restraints excluded: chain H residue   60 LEU
Chi-restraints excluded: chain H residue   79 ARG
Chi-restraints excluded: chain H residue   84 ILE
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   19 ASN
Chi-restraints excluded: chain L residue   38 THR
Chi-restraints excluded: chain L residue   51 VAL
Chi-restraints excluded: chain L residue   63 THR
Chi-restraints excluded: chain L residue   66 ILE
Chi-restraints excluded: chain L residue  118 VAL
Chi-restraints excluded: chain P residue   20 VAL
Chi-restraints excluded: chain Q residue   66 LEU
Chi-restraints excluded: chain T residue   85 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 190 optimal weight:   10.0000
   chunk 57 optimal weight:    5.9990
   chunk 112 optimal weight:    1.9990
   chunk 45 optimal weight:   30.0000
   chunk 72 optimal weight:    0.5980
   chunk 171 optimal weight:   30.0000
   chunk 162 optimal weight:    3.9990
   chunk 156 optimal weight:    8.9990
   chunk 41 optimal weight:    8.9990
   chunk 86 optimal weight:    2.9990
   chunk 187 optimal weight:    3.9990
   overall best weight:    2.7188

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

Flipped N/Q/H residues before XYZ refinement:
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  81 ASN
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.151375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.124807 restraints weight = 48013.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3935 rms_B_bonded: 0.85
r_work: 0.3583 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3534 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.2403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051  31478  Z= 0.309
  Angle     :  0.698  16.352  47296  Z= 0.349
  Chirality :  0.040   0.263   6056
  Planarity :  0.005   0.047   2401
  Dihedral  : 24.432 178.732  16228
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 18.53 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.16 (0.26), residues: 1017
  helix:  0.88 (0.26), residues: 389
  sheet: -2.22 (0.39), residues: 152
  loop : -1.67 (0.27), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG H 116 
 TYR   0.017   0.002   TYR F  25 
 PHE   0.011   0.001   PHE P  32 
 TRP   0.010   0.001   TRP Q  72 
 HIS   0.006   0.001   HIS P   9 

Details of bonding type rmsd
  covalent geometry    : bond        0.00599 (31478)
  covalent geometry    : angle       0.69788 (47296)
  hydrogen bonds       : bond        0.09544 ( 1201)
  hydrogen bonds       : angle       3.34673 ( 2309)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 97
  time to evaluate  : 0.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   67 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8588 (mp)
REVERT: F    9 MET cc_start: -0.2023 (pmt) cc_final: -0.2568 (pmm)
REVERT: H   79 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8212 (ptm-80)
REVERT: P    5 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.7759 (ptp-170)
  outliers start: 31
  outliers final: 19
  residues processed: 118
  average time/residue: 0.7028
  time to fit residues: 96.9560
Evaluate side-chains
  117 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  106 PHE
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain F residue   23 GLU
Chi-restraints excluded: chain H residue   60 LEU
Chi-restraints excluded: chain H residue   79 ARG
Chi-restraints excluded: chain H residue   84 ILE
Chi-restraints excluded: chain H residue  102 VAL
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   19 ASN
Chi-restraints excluded: chain L residue   38 THR
Chi-restraints excluded: chain L residue   51 VAL
Chi-restraints excluded: chain L residue   63 THR
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   66 ILE
Chi-restraints excluded: chain L residue  118 VAL
Chi-restraints excluded: chain P residue    5 ARG
Chi-restraints excluded: chain P residue   20 VAL
Chi-restraints excluded: chain Q residue   12 VAL
Chi-restraints excluded: chain Q residue   66 LEU
Chi-restraints excluded: chain T residue   85 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 135 optimal weight:    1.9990
   chunk 10 optimal weight:    0.3980
   chunk 4 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 147 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 162 optimal weight:    3.9990
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.154238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.128379 restraints weight = 48564.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3996 rms_B_bonded: 0.53
r_work: 0.3635 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3587 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.3073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  31478  Z= 0.142
  Angle     :  0.588  16.573  47296  Z= 0.297
  Chirality :  0.033   0.239   6056
  Planarity :  0.004   0.053   2401
  Dihedral  : 24.215 179.336  16228
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 19.46 %
    Favored  : 77.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.82 (0.26), residues: 1017
  helix:  1.22 (0.26), residues: 389
  sheet: -1.94 (0.42), residues: 143
  loop : -1.58 (0.27), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG H 116 
 TYR   0.018   0.001   TYR F  25 
 PHE   0.008   0.001   PHE P  32 
 TRP   0.006   0.001   TRP P  60 
 HIS   0.005   0.001   HIS O  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (31478)
  covalent geometry    : angle       0.58831 (47296)
  hydrogen bonds       : bond        0.08366 ( 1201)
  hydrogen bonds       : angle       3.12959 ( 2309)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   67 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8408 (mp)
REVERT: F    9 MET cc_start: -0.2097 (pmt) cc_final: -0.2645 (pmm)
REVERT: P    5 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.7766 (ptp-170)
  outliers start: 25
  outliers final: 14
  residues processed: 121
  average time/residue: 0.7493
  time to fit residues: 105.1035
Evaluate side-chains
  114 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  106 PHE
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain F residue   23 GLU
Chi-restraints excluded: chain H residue   60 LEU
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   19 ASN
Chi-restraints excluded: chain L residue   38 THR
Chi-restraints excluded: chain L residue   51 VAL
Chi-restraints excluded: chain L residue   63 THR
Chi-restraints excluded: chain L residue  118 VAL
Chi-restraints excluded: chain P residue    5 ARG
Chi-restraints excluded: chain P residue   20 VAL
Chi-restraints excluded: chain Q residue   66 LEU
Chi-restraints excluded: chain T residue   85 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 96 optimal weight:    1.9990
   chunk 91 optimal weight:    8.9990
   chunk 78 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 188 optimal weight:   10.0000
   chunk 68 optimal weight:    7.9990
   chunk 85 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   chunk 167 optimal weight:   50.0000
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 197 HIS
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.152936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.127345 restraints weight = 47993.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3976 rms_B_bonded: 0.58
r_work: 0.3617 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3568 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.3012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  31478  Z= 0.202
  Angle     :  0.625  18.501  47296  Z= 0.314
  Chirality :  0.035   0.247   6056
  Planarity :  0.005   0.050   2401
  Dihedral  : 24.229 179.384  16228
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 20.98 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.77 (0.26), residues: 1017
  helix:  1.23 (0.26), residues: 389
  sheet: -1.88 (0.41), residues: 148
  loop : -1.52 (0.27), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG H 116 
 TYR   0.018   0.001   TYR F  25 
 PHE   0.011   0.001   PHE P  32 
 TRP   0.007   0.001   TRP Q  72 
 HIS   0.005   0.001   HIS O  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 (31478)
  covalent geometry    : angle       0.62542 (47296)
  hydrogen bonds       : bond        0.08704 ( 1201)
  hydrogen bonds       : angle       3.17446 ( 2309)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   67 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8503 (mp)
REVERT: F    9 MET cc_start: -0.1899 (pmt) cc_final: -0.2550 (pmm)
REVERT: F   88 MET cc_start: -0.0445 (mpt) cc_final: -0.3011 (tmm)
REVERT: P    5 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.7699 (ptp-170)
  outliers start: 22
  outliers final: 16
  residues processed: 114
  average time/residue: 0.7078
  time to fit residues: 94.1346
Evaluate side-chains
  116 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  106 PHE
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain F residue   23 GLU
Chi-restraints excluded: chain H residue   60 LEU
Chi-restraints excluded: chain H residue   84 ILE
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   19 ASN
Chi-restraints excluded: chain L residue   38 THR
Chi-restraints excluded: chain L residue   51 VAL
Chi-restraints excluded: chain L residue   63 THR
Chi-restraints excluded: chain L residue   66 ILE
Chi-restraints excluded: chain L residue  118 VAL
Chi-restraints excluded: chain P residue    5 ARG
Chi-restraints excluded: chain P residue   20 VAL
Chi-restraints excluded: chain Q residue   66 LEU
Chi-restraints excluded: chain T residue   85 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 155 optimal weight:   10.0000
   chunk 195 optimal weight:   30.0000
   chunk 19 optimal weight:    6.9990
   chunk 109 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 127 optimal weight:    5.9990
   chunk 42 optimal weight:   10.0000
   chunk 31 optimal weight:    2.9990
   chunk 67 optimal weight:    8.9990
   chunk 140 optimal weight:    6.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    2.9786

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

Flipped N/Q/H residues before XYZ refinement:
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.151365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.124344 restraints weight = 47708.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3941 rms_B_bonded: 0.90
r_work: 0.3582 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3534 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.2734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  31478  Z= 0.334
  Angle     :  0.723  20.283  47296  Z= 0.359
  Chirality :  0.040   0.265   6056
  Planarity :  0.005   0.051   2401
  Dihedral  : 24.359 178.813  16228
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 21.45 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.90 (0.26), residues: 1017
  helix:  1.03 (0.26), residues: 389
  sheet: -2.05 (0.40), residues: 146
  loop : -1.48 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG H 116 
 TYR   0.024   0.002   TYR D  75 
 PHE   0.010   0.001   PHE P  32 
 TRP   0.010   0.001   TRP Q  72 
 HIS   0.006   0.001   HIS P   9 

Details of bonding type rmsd
  covalent geometry    : bond        0.00650 (31478)
  covalent geometry    : angle       0.72333 (47296)
  hydrogen bonds       : bond        0.09713 ( 1201)
  hydrogen bonds       : angle       3.31113 ( 2309)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   67 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8608 (mp)
REVERT: D  125 ASN cc_start: 0.8696 (m-40) cc_final: 0.8368 (m-40)
REVERT: F    9 MET cc_start: -0.1858 (pmt) cc_final: -0.2516 (pmm)
REVERT: F   88 MET cc_start: -0.0334 (mpt) cc_final: -0.2898 (tmm)
REVERT: P    5 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.7743 (ptp-170)
  outliers start: 18
  outliers final: 16
  residues processed: 111
  average time/residue: 0.6787
  time to fit residues: 87.9170
Evaluate side-chains
  116 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  106 PHE
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  195 ASN
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain F residue   23 GLU
Chi-restraints excluded: chain H residue   60 LEU
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   19 ASN
Chi-restraints excluded: chain L residue   38 THR
Chi-restraints excluded: chain L residue   51 VAL
Chi-restraints excluded: chain L residue   63 THR
Chi-restraints excluded: chain L residue   66 ILE
Chi-restraints excluded: chain L residue  118 VAL
Chi-restraints excluded: chain P residue    5 ARG
Chi-restraints excluded: chain P residue   20 VAL
Chi-restraints excluded: chain Q residue   66 LEU
Chi-restraints excluded: chain T residue   85 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 111 optimal weight:    2.9990
   chunk 69 optimal weight:    8.9990
   chunk 97 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 113 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   chunk 144 optimal weight:    1.9990
   chunk 20 optimal weight:   20.0000
   chunk 35 optimal weight:    7.9990
   chunk 7 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 100 ASN
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.153288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.127257 restraints weight = 48346.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3987 rms_B_bonded: 0.55
r_work: 0.3636 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3590 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.3143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074  31478  Z= 0.184
  Angle     :  0.618  20.836  47296  Z= 0.311
  Chirality :  0.034   0.246   6056
  Planarity :  0.005   0.050   2401
  Dihedral  : 24.222 179.094  16228
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 21.21 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.68 (0.26), residues: 1017
  helix:  1.24 (0.26), residues: 389
  sheet: -1.80 (0.40), residues: 149
  loop : -1.43 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG H 116 
 TYR   0.020   0.001   TYR F  25 
 PHE   0.010   0.001   PHE P  32 
 TRP   0.006   0.001   TRP Q  72 
 HIS   0.005   0.001   HIS O  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (31478)
  covalent geometry    : angle       0.61841 (47296)
  hydrogen bonds       : bond        0.08485 ( 1201)
  hydrogen bonds       : angle       3.16491 ( 2309)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8508.83 seconds
wall clock time: 146 minutes 19.57 seconds (8779.57 seconds total)