Starting phenix.real_space_refine (version: dev)
on Tue Nov 29 11:44:18 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6peo_20328/11_2022/6peo_20328.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6peo_20328/11_2022/6peo_20328.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6peo_20328/11_2022/6peo_20328.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6peo_20328/11_2022/6peo_20328.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6peo_20328/11_2022/6peo_20328.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6peo_20328/11_2022/6peo_20328.pdb"
  }
  resolution = 3.3
  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
-------------------------------------------------------------------------------
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=   1.000
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
Convert atoms to be neutral
Process input model

  Symmetric amino acids flipped
    Residue "A PHE   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP   98": "OD1" <-> "OD2"
    Residue "B PHE   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP   98": "OD1" <-> "OD2"
    Residue "C PHE   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP   98": "OD1" <-> "OD2"
    Residue "D PHE   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ASP   98": "OD1" <-> "OD2"
    Residue "E PHE   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ASP   98": "OD1" <-> "OD2"
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib"
  Total number of atoms: 2205
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 441
          Classifications: {'peptide': 64}
          Link IDs: {'TRANS': 63}
    Chain: "B"
      Number of atoms: 441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 441
          Classifications: {'peptide': 64}
          Link IDs: {'TRANS': 63}
    Chain: "C"
      Number of atoms: 441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 441
          Classifications: {'peptide': 64}
          Link IDs: {'TRANS': 63}
    Chain: "D"
      Number of atoms: 441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 441
          Classifications: {'peptide': 64}
          Link IDs: {'TRANS': 63}
    Chain: "E"
      Number of atoms: 441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 441
          Classifications: {'peptide': 64}
          Link IDs: {'TRANS': 63}
  Time building chain proxies: 1.65, per 1000 atoms: 0.75
  Number of scatterers: 2205
  At special positions: 0
  Unit cell: (74.55, 60.705, 39.405, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     450      8.00
     N     380      7.00
     C    1375      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  - 3.50
        Amino acid           : False - 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: 0.98
  Conformation dependent library (CDL) restraints added in 366.6 milliseconds
  

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  540

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 5 sheets defined
      0.0% alpha, 70.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 37 through 40
      removed outlier: 6.490A  pdb=" N   VAL A  37 " --> pdb=" O   LEU C  38 " (cutoff:3.500A)
      removed outlier: 7.839A  pdb=" N   VAL C  40 " --> pdb=" O   VAL A  37 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   TYR A  39 " --> pdb=" O   VAL C  40 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   VAL C  37 " --> pdb=" O   LEU E  38 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   VAL E  40 " --> pdb=" O   VAL C  37 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   TYR C  39 " --> pdb=" O   VAL E  40 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 43 through 66
      removed outlier: 6.774A  pdb=" N   VAL D  48 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   VAL B  49 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   GLN D  50 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   GLU B  61 " --> pdb=" O   LYS D  60 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   GLN D  62 " --> pdb=" O   GLU B  61 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   VAL B  63 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   THR D  64 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   ASN B  65 " --> pdb=" O   THR D  64 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   VAL D  66 " --> pdb=" O   ASN B  65 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   VAL B  48 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   VAL A  49 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   GLN B  50 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   GLU A  61 " --> pdb=" O   LYS B  60 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   GLN B  62 " --> pdb=" O   GLU A  61 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   VAL A  63 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   THR B  64 " --> pdb=" O   VAL A  63 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   ASN A  65 " --> pdb=" O   THR B  64 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   VAL B  66 " --> pdb=" O   ASN A  65 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   THR A  44 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 8.028A  pdb=" N   GLY C  47 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
      removed outlier: 8.418A  pdb=" N   GLU A  46 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 8.290A  pdb=" N   VAL C  49 " --> pdb=" O   GLU A  46 " (cutoff:3.500A)
      removed outlier: 8.988A  pdb=" N   VAL A  48 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 9.176A  pdb=" N   GLY C  51 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 5.959A  pdb=" N   GLN A  50 " --> pdb=" O   GLY C  51 " (cutoff:3.500A)
      removed outlier: 7.521A  pdb=" N   ALA C  53 " --> pdb=" O   GLN A  50 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   VAL A  52 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 7.964A  pdb=" N   VAL C  55 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   THR A  54 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
      removed outlier: 8.009A  pdb=" N   GLU C  57 " --> pdb=" O   THR A  54 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   ALA A  56 " --> pdb=" O   GLU C  57 " (cutoff:3.500A)
      removed outlier: 8.140A  pdb=" N   THR C  59 " --> pdb=" O   ALA A  56 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   LYS A  58 " --> pdb=" O   THR C  59 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   GLU C  61 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
      removed outlier: 7.804A  pdb=" N   LYS A  60 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
      removed outlier: 10.371A  pdb=" N   VAL C  63 " --> pdb=" O   LYS A  60 " (cutoff:3.500A)
      removed outlier: 9.088A  pdb=" N   GLN A  62 " --> pdb=" O   VAL C  63 " (cutoff:3.500A)
      removed outlier: 9.883A  pdb=" N   ASN C  65 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      removed outlier: 8.997A  pdb=" N   THR A  64 " --> pdb=" O   ASN C  65 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   THR C  44 " --> pdb=" O   LYS E  45 " (cutoff:3.500A)
      removed outlier: 8.026A  pdb=" N   GLY E  47 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      removed outlier: 8.414A  pdb=" N   GLU C  46 " --> pdb=" O   GLY E  47 " (cutoff:3.500A)
      removed outlier: 8.285A  pdb=" N   VAL E  49 " --> pdb=" O   GLU C  46 " (cutoff:3.500A)
      removed outlier: 8.982A  pdb=" N   VAL C  48 " --> pdb=" O   VAL E  49 " (cutoff:3.500A)
      removed outlier: 9.174A  pdb=" N   GLY E  51 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 5.956A  pdb=" N   GLN C  50 " --> pdb=" O   GLY E  51 " (cutoff:3.500A)
      removed outlier: 7.517A  pdb=" N   ALA E  53 " --> pdb=" O   GLN C  50 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   VAL C  52 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 7.961A  pdb=" N   VAL E  55 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   THR C  54 " --> pdb=" O   VAL E  55 " (cutoff:3.500A)
      removed outlier: 8.006A  pdb=" N   GLU E  57 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   ALA C  56 " --> pdb=" O   GLU E  57 " (cutoff:3.500A)
      removed outlier: 8.137A  pdb=" N   THR E  59 " --> pdb=" O   ALA C  56 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   LYS C  58 " --> pdb=" O   THR E  59 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   GLU E  61 " --> pdb=" O   LYS C  58 " (cutoff:3.500A)
      removed outlier: 7.804A  pdb=" N   LYS C  60 " --> pdb=" O   GLU E  61 " (cutoff:3.500A)
      removed outlier: 10.372A  pdb=" N   VAL E  63 " --> pdb=" O   LYS C  60 " (cutoff:3.500A)
      removed outlier: 9.088A  pdb=" N   GLN C  62 " --> pdb=" O   VAL E  63 " (cutoff:3.500A)
      removed outlier: 9.882A  pdb=" N   ASN E  65 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
      removed outlier: 8.995A  pdb=" N   THR C  64 " --> pdb=" O   ASN E  65 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 69 through 71
      removed outlier: 6.460A  pdb=" N   VAL A  70 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   VAL C  70 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 74 through 83
      removed outlier: 6.964A  pdb=" N   THR B  81 " --> pdb=" O   LYS D  80 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   VAL D  82 " --> pdb=" O   THR B  81 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   GLU B  83 " --> pdb=" O   VAL D  82 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   THR A  81 " --> pdb=" O   LYS B  80 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   VAL B  82 " --> pdb=" O   THR A  81 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   GLU A  83 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   VAL A  74 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 7.850A  pdb=" N   VAL C  77 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   ALA A  76 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   GLN C  79 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   ALA A  78 " --> pdb=" O   GLN C  79 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   THR C  81 " --> pdb=" O   ALA A  78 " (cutoff:3.500A)
      removed outlier: 7.683A  pdb=" N   LYS A  80 " --> pdb=" O   THR C  81 " (cutoff:3.500A)
      removed outlier: 10.229A  pdb=" N   GLU C  83 " --> pdb=" O   LYS A  80 " (cutoff:3.500A)
      removed outlier: 8.997A  pdb=" N   VAL A  82 " --> pdb=" O   GLU C  83 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   VAL C  74 " --> pdb=" O   THR E  75 " (cutoff:3.500A)
      removed outlier: 7.852A  pdb=" N   VAL E  77 " --> pdb=" O   VAL C  74 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   ALA C  76 " --> pdb=" O   VAL E  77 " (cutoff:3.500A)
      removed outlier: 8.018A  pdb=" N   GLN E  79 " --> pdb=" O   ALA C  76 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   ALA C  78 " --> pdb=" O   GLN E  79 " (cutoff:3.500A)
      removed outlier: 7.615A  pdb=" N   THR E  81 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 7.681A  pdb=" N   LYS C  80 " --> pdb=" O   THR E  81 " (cutoff:3.500A)
      removed outlier: 10.227A  pdb=" N   GLU E  83 " --> pdb=" O   LYS C  80 " (cutoff:3.500A)
      removed outlier: 8.994A  pdb=" N   VAL C  82 " --> pdb=" O   GLU E  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 96
      removed outlier: 8.242A  pdb=" N   ALA B  89 " --> pdb=" O   ALA D  90 " (cutoff:3.500A)
      removed outlier: 7.942A  pdb=" N   THR D  92 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
      removed outlier: 9.018A  pdb=" N   ALA B  91 " --> pdb=" O   THR D  92 " (cutoff:3.500A)
      removed outlier: 8.530A  pdb=" N   PHE D  94 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   GLY B  93 " --> pdb=" O   PHE D  94 " (cutoff:3.500A)
      removed outlier: 7.916A  pdb=" N   LYS D  96 " --> pdb=" O   GLY B  93 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   VAL B  95 " --> pdb=" O   LYS D  96 " (cutoff:3.500A)
      removed outlier: 8.241A  pdb=" N   ALA A  89 " --> pdb=" O   ALA B  90 " (cutoff:3.500A)
      removed outlier: 7.941A  pdb=" N   THR B  92 " --> pdb=" O   ALA A  89 " (cutoff:3.500A)
      removed outlier: 9.017A  pdb=" N   ALA A  91 " --> pdb=" O   THR B  92 " (cutoff:3.500A)
      removed outlier: 8.529A  pdb=" N   PHE B  94 " --> pdb=" O   ALA A  91 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   GLY A  93 " --> pdb=" O   PHE B  94 " (cutoff:3.500A)
      removed outlier: 7.917A  pdb=" N   LYS B  96 " --> pdb=" O   GLY A  93 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   VAL A  95 " --> pdb=" O   LYS B  96 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   ALA C  91 " --> pdb=" O   ALA A  90 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   THR A  92 " --> pdb=" O   ALA C  91 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   GLY C  93 " --> pdb=" O   THR A  92 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   ALA E  91 " --> pdb=" O   ALA C  90 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   THR C  92 " --> pdb=" O   ALA E  91 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   GLY E  93 " --> pdb=" O   THR C  92 " (cutoff:3.500A)

    60 hydrogen bonds defined for protein.
    180 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.50

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 395
        1.29 -     1.36: 340
        1.36 -     1.42: 75
        1.42 -     1.49: 374
        1.49 -     1.55: 1026
  Bond restraints: 2210
  Sorted by residual:
  bond pdb=" CA  GLU B  57 "
       pdb=" CB  GLU B  57 "
    ideal  model  delta    sigma   weight residual
    1.530  1.515  0.015 1.50e-02 4.44e+03 1.01e+00
  bond pdb=" CA  GLU E  57 "
       pdb=" CB  GLU E  57 "
    ideal  model  delta    sigma   weight residual
    1.530  1.516  0.015 1.50e-02 4.44e+03 9.49e-01
  bond pdb=" CA  GLU D  57 "
       pdb=" CB  GLU D  57 "
    ideal  model  delta    sigma   weight residual
    1.530  1.516  0.015 1.50e-02 4.44e+03 9.36e-01
  bond pdb=" CA  GLU A  57 "
       pdb=" CB  GLU A  57 "
    ideal  model  delta    sigma   weight residual
    1.530  1.516  0.014 1.50e-02 4.44e+03 9.19e-01
  bond pdb=" CA  GLU C  57 "
       pdb=" CB  GLU C  57 "
    ideal  model  delta    sigma   weight residual
    1.530  1.517  0.014 1.50e-02 4.44e+03 8.56e-01
  ... (remaining 2205 not shown)

  Histogram of bond angle deviations from ideal:
      106.29 -   109.75: 308
      109.75 -   113.21: 1048
      113.21 -   116.67: 386
      116.67 -   120.13: 229
      120.13 -   123.59: 1014
  Bond angle restraints: 2985
  Sorted by residual:
  angle pdb=" N   GLU B  61 "
        pdb=" CA  GLU B  61 "
        pdb=" CB  GLU B  61 "
      ideal   model   delta    sigma   weight residual
     110.69  113.10   -2.41 1.61e+00 3.86e-01 2.25e+00
  angle pdb=" N   GLU A  61 "
        pdb=" CA  GLU A  61 "
        pdb=" CB  GLU A  61 "
      ideal   model   delta    sigma   weight residual
     110.69  113.08   -2.39 1.61e+00 3.86e-01 2.21e+00
  angle pdb=" N   GLU C  61 "
        pdb=" CA  GLU C  61 "
        pdb=" CB  GLU C  61 "
      ideal   model   delta    sigma   weight residual
     110.69  113.08   -2.39 1.61e+00 3.86e-01 2.20e+00
  angle pdb=" N   GLU E  61 "
        pdb=" CA  GLU E  61 "
        pdb=" CB  GLU E  61 "
      ideal   model   delta    sigma   weight residual
     110.69  113.07   -2.38 1.61e+00 3.86e-01 2.19e+00
  angle pdb=" N   GLU D  61 "
        pdb=" CA  GLU D  61 "
        pdb=" CB  GLU D  61 "
      ideal   model   delta    sigma   weight residual
     110.69  113.07   -2.38 1.61e+00 3.86e-01 2.18e+00
  ... (remaining 2980 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.41: 1168
       13.41 -    26.82: 97
       26.82 -    40.23: 10
       40.23 -    53.64: 20
       53.64 -    67.05: 5
  Dihedral angle restraints: 1300
    sinusoidal: 440
      harmonic: 860
  Sorted by residual:
  dihedral pdb=" CA  LYS A  60 "
           pdb=" C   LYS A  60 "
           pdb=" N   GLU A  61 "
           pdb=" CA  GLU A  61 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.58   18.42     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  LYS C  60 "
           pdb=" C   LYS C  60 "
           pdb=" N   GLU C  61 "
           pdb=" CA  GLU C  61 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.61   18.39     0      5.00e+00 4.00e-02 1.35e+01
  dihedral pdb=" CA  LYS E  60 "
           pdb=" C   LYS E  60 "
           pdb=" N   GLU E  61 "
           pdb=" CA  GLU E  61 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.61   18.39     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 1297 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 188
       0.027 -    0.054: 100
       0.054 -    0.082: 30
       0.082 -    0.109: 48
       0.109 -    0.136: 24
  Chirality restraints: 390
  Sorted by residual:
  chirality pdb=" CA  VAL E  49 "
            pdb=" N   VAL E  49 "
            pdb=" C   VAL E  49 "
            pdb=" CB  VAL E  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.63e-01
  chirality pdb=" CA  VAL C  49 "
            pdb=" N   VAL C  49 "
            pdb=" C   VAL C  49 "
            pdb=" CB  VAL C  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.58e-01
  chirality pdb=" CA  VAL D  49 "
            pdb=" N   VAL D  49 "
            pdb=" C   VAL D  49 "
            pdb=" CB  VAL D  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.58e-01
  ... (remaining 387 not shown)

  Planarity restraints: 375
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B  60 "   -0.020 2.00e-02 2.50e+03   3.99e-02 1.59e+01
        pdb=" C   LYS B  60 "    0.069 2.00e-02 2.50e+03
        pdb=" O   LYS B  60 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   GLU B  61 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A  60 "   -0.020 2.00e-02 2.50e+03   3.99e-02 1.59e+01
        pdb=" C   LYS A  60 "    0.069 2.00e-02 2.50e+03
        pdb=" O   LYS A  60 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   GLU A  61 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C  60 "   -0.020 2.00e-02 2.50e+03   3.98e-02 1.59e+01
        pdb=" C   LYS C  60 "    0.069 2.00e-02 2.50e+03
        pdb=" O   LYS C  60 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   GLU C  61 "   -0.023 2.00e-02 2.50e+03
  ... (remaining 372 not shown)

  Histogram of nonbonded interaction distances:
        2.49 -     2.97: 1220
        2.97 -     3.46: 1883
        3.46 -     3.94: 3420
        3.94 -     4.42: 3801
        4.42 -     4.90: 7503
  Nonbonded interactions: 17827
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS B  58 "
            pdb=" OE1 GLU B  61 "
     model   vdw
     2.492 2.520
  nonbonded pdb=" NZ  LYS E  58 "
            pdb=" OE1 GLU E  61 "
     model   vdw
     2.492 2.520
  nonbonded pdb=" NZ  LYS D  58 "
            pdb=" OE1 GLU D  61 "
     model   vdw
     2.492 2.520
  nonbonded pdb=" NZ  LYS C  58 "
            pdb=" OE1 GLU C  61 "
     model   vdw
     2.492 2.520
  nonbonded pdb=" NZ  LYS A  58 "
            pdb=" OE1 GLU A  61 "
     model   vdw
     2.492 2.520
  ... (remaining 17822 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    1375      2.51       5
     N     380      2.21       5
     O     450      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
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:             0.100
  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:             0.000
  Extract box with map and model:          0.670
  Check model and map are aligned:         0.030
  Convert atoms to be neutral:             0.020
  Process input model:                     11.240
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Set scattering table:                    0.010
  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:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.015   2210  Z= 0.198
  Angle     :  0.543   3.112   2985  Z= 0.309
  Chirality :  0.054   0.136    390
  Planarity :  0.007   0.040    375
  Dihedral  : 13.058  67.049    760
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.68 %
    Favored  : 90.32 %
  Rotamer Outliers :  0.00 %
  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: -1.64 (0.42), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.24 (0.32), residues: 310

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 225 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.217 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.1618
  time to fit residues: 8.9901
Evaluate side-chains
  34 residues out of total 225 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.236 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.3415
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 22 optimal weight:    8.9990
   chunk 12 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 15 optimal weight:    9.9990
   chunk 23 optimal weight:    0.3980
   chunk 9 optimal weight:   20.0000
   chunk 14 optimal weight:   20.0000
   chunk 17 optimal weight:   20.0000
   chunk 27 optimal weight:    0.7980
   chunk 8 optimal weight:   10.0000
   overall best weight:    5.8386

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

Flipped N/Q/H residues before XYZ refinement:
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.2109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.025   2210  Z= 0.357
  Angle     :  0.533   3.705   2985  Z= 0.305
  Chirality :  0.057   0.136    390
  Planarity :  0.002   0.014    375
  Dihedral  :  4.925  13.939    320
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.03 %
    Favored  : 90.97 %
  Rotamer Outliers :  3.56 %
  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: -1.57 (0.40), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.19 (0.31), residues: 310

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 225 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 36
  time to evaluate  : 0.251 
Fit side-chains
  outliers start: 8
  outliers final: 4
  residues processed: 42
  average time/residue: 0.1534
  time to fit residues: 7.5875
Evaluate side-chains
  39 residues out of total 225 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.250 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0302
  time to fit residues: 0.5301
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 18 optimal weight:    9.9990
   chunk 7 optimal weight:    0.8980
   chunk 27 optimal weight:   10.0000
   chunk 29 optimal weight:   10.0000
   chunk 24 optimal weight:    8.9990
   chunk 9 optimal weight:    9.9990
   chunk 21 optimal weight:    8.9990
   chunk 26 optimal weight:    9.9990
   chunk 20 optimal weight:    0.0770
   chunk 14 optimal weight:    9.9990
   overall best weight:    3.9944

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.020   2210  Z= 0.257
  Angle     :  0.472   3.231   2985  Z= 0.268
  Chirality :  0.054   0.127    390
  Planarity :  0.002   0.011    375
  Dihedral  :  4.589  12.582    320
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer Outliers :  3.11 %
  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: -1.73 (0.40), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.31 (0.30), residues: 310

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 225 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 35
  time to evaluate  : 0.261 
Fit side-chains
  outliers start: 7
  outliers final: 4
  residues processed: 39
  average time/residue: 0.1626
  time to fit residues: 7.4359
Evaluate side-chains
  36 residues out of total 225 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 32
  time to evaluate  : 0.252 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0304
  time to fit residues: 0.5292
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 3 optimal weight:    7.9990
   chunk 13 optimal weight:    9.9990
   chunk 18 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   chunk 28 optimal weight:   10.0000
   chunk 14 optimal weight:   10.0000
   chunk 25 optimal weight:    4.9990
   chunk 7 optimal weight:    9.9990
   chunk 24 optimal weight:   10.0000
   chunk 16 optimal weight:    5.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
E  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.2837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.027   2210  Z= 0.423
  Angle     :  0.552   3.515   2985  Z= 0.315
  Chirality :  0.057   0.133    390
  Planarity :  0.002   0.012    375
  Dihedral  :  4.729  13.174    320
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.68 %
    Favored  : 90.32 %
  Rotamer Outliers :  4.00 %
  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: -2.10 (0.38), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.59 (0.29), residues: 310

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 225 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 32
  time to evaluate  : 0.267 
Fit side-chains
  outliers start: 9
  outliers final: 5
  residues processed: 37
  average time/residue: 0.1570
  time to fit residues: 6.8656
Evaluate side-chains
  35 residues out of total 225 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 30
  time to evaluate  : 0.251 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0330
  time to fit residues: 0.5861
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 11 optimal weight:   20.0000
   chunk 24 optimal weight:    7.9990
   chunk 20 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 26 optimal weight:    6.9990
   chunk 7 optimal weight:   10.0000
   chunk 9 optimal weight:    8.9990
   chunk 5 optimal weight:    0.0470
   chunk 17 optimal weight:    0.1980
   overall best weight:    3.8484

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.2877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2210  Z= 0.245
  Angle     :  0.475   3.872   2985  Z= 0.271
  Chirality :  0.054   0.128    390
  Planarity :  0.002   0.013    375
  Dihedral  :  4.401  13.330    320
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer Outliers :  4.44 %
  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: -2.18 (0.38), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.65 (0.29), residues: 310

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 225 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 36
  time to evaluate  : 0.272 
Fit side-chains
  outliers start: 10
  outliers final: 2
  residues processed: 43
  average time/residue: 0.1413
  time to fit residues: 7.2828
Evaluate side-chains
  36 residues out of total 225 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 34
  time to evaluate  : 0.274 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0509
  time to fit residues: 0.5043
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 29 optimal weight:    9.9990
   chunk 24 optimal weight:    7.9990
   chunk 13 optimal weight:    9.9990
   chunk 2 optimal weight:   20.0000
   chunk 9 optimal weight:    9.9990
   chunk 15 optimal weight:    9.9990
   chunk 27 optimal weight:    7.9990
   chunk 3 optimal weight:    5.9990
   chunk 16 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    6.5988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.3068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.027   2210  Z= 0.403
  Angle     :  0.548   4.251   2985  Z= 0.309
  Chirality :  0.056   0.133    390
  Planarity :  0.002   0.010    375
  Dihedral  :  4.621  14.239    320
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.68 %
    Favored  : 90.32 %
  Rotamer Outliers :  2.22 %
  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: -2.30 (0.37), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.75 (0.28), residues: 310

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 225 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.234 
Fit side-chains
  outliers start: 5
  outliers final: 3
  residues processed: 33
  average time/residue: 0.1562
  time to fit residues: 6.1174
Evaluate side-chains
  35 residues out of total 225 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 32
  time to evaluate  : 0.259 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.1235
  time to fit residues: 0.7711
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 24 optimal weight:   10.0000
   chunk 28 optimal weight:    5.9990
   chunk 18 optimal weight:    8.9990
   chunk 17 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 11 optimal weight:   10.0000
   chunk 8 optimal weight:   20.0000
   chunk 5 optimal weight:    5.9990
   chunk 19 optimal weight:    8.9990
   chunk 14 optimal weight:    6.9990
   overall best weight:    5.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.3085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.026   2210  Z= 0.323
  Angle     :  0.513   4.560   2985  Z= 0.290
  Chirality :  0.054   0.137    390
  Planarity :  0.002   0.009    375
  Dihedral  :  4.494  14.082    320
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.74 %
    Favored  : 92.26 %
  Rotamer Outliers :  1.78 %
  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: -2.35 (0.37), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.28), residues: 310

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 225 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 32
  time to evaluate  : 0.247 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 33
  average time/residue: 0.1613
  time to fit residues: 6.3005
Evaluate side-chains
  35 residues out of total 225 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 32
  time to evaluate  : 0.244 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0342
  time to fit residues: 0.4317
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 22 optimal weight:   20.0000
   chunk 26 optimal weight:    9.9990
   chunk 27 optimal weight:    7.9990
   chunk 25 optimal weight:    9.9990
   chunk 16 optimal weight:    9.9990
   chunk 11 optimal weight:   10.0000
   chunk 21 optimal weight:    9.9990
   chunk 8 optimal weight:    5.9990
   chunk 24 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   overall best weight:    8.7990

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.3155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.008   0.031   2210  Z= 0.521
  Angle     :  0.596   4.145   2985  Z= 0.338
  Chirality :  0.058   0.139    390
  Planarity :  0.002   0.009    375
  Dihedral  :  4.831  14.906    320
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.68 %
    Favored  : 90.32 %
  Rotamer Outliers :  1.78 %
  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: -2.55 (0.37), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.93 (0.28), residues: 310

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 225 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 29
  time to evaluate  : 0.234 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 31
  average time/residue: 0.1747
  time to fit residues: 6.4325
Evaluate side-chains
  32 residues out of total 225 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 29
  time to evaluate  : 0.259 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0260
  time to fit residues: 0.4774
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 17 optimal weight:   10.0000
   chunk 13 optimal weight:    7.9990
   chunk 19 optimal weight:   10.0000
   chunk 29 optimal weight:    0.7980
   chunk 27 optimal weight:    8.9990
   chunk 23 optimal weight:    8.9990
   chunk 2 optimal weight:    9.9990
   chunk 18 optimal weight:    7.9990
   chunk 14 optimal weight:    5.9990
   chunk 25 optimal weight:    6.9990
   overall best weight:    4.7588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.3198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2210  Z= 0.301
  Angle     :  0.515   4.802   2985  Z= 0.291
  Chirality :  0.055   0.138    390
  Planarity :  0.002   0.009    375
  Dihedral  :  4.467  14.342    320
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer Outliers :  0.89 %
  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: -2.52 (0.37), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.91 (0.28), residues: 310

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 225 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 32
  time to evaluate  : 0.207 
Fit side-chains
  outliers start: 2
  outliers final: 0
  residues processed: 34
  average time/residue: 0.1559
  time to fit residues: 6.2137
Evaluate side-chains
  32 residues out of total 225 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.280 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.2986
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 21 optimal weight:    9.9990
   chunk 3 optimal weight:   20.0000
   chunk 6 optimal weight:    7.9990
   chunk 23 optimal weight:    9.9990
   chunk 9 optimal weight:    7.9990
   chunk 24 optimal weight:   10.0000
   chunk 4 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 17 optimal weight:    8.9990
   overall best weight:    7.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.3256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.007   0.033   2210  Z= 0.445
  Angle     :  0.571   5.163   2985  Z= 0.323
  Chirality :  0.057   0.137    390
  Planarity :  0.002   0.009    375
  Dihedral  :  4.656  14.652    320
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.68 %
    Favored  : 90.32 %
  Rotamer Outliers :  0.89 %
  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: -2.62 (0.37), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.98 (0.28), residues: 310

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 225 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 30
  time to evaluate  : 0.367 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 31
  average time/residue: 0.1377
  time to fit residues: 5.0464
Evaluate side-chains
  31 residues out of total 225 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 30
  time to evaluate  : 0.194 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0441
  time to fit residues: 0.3227
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    8.9990
   chunk 16 optimal weight:    6.9990
   chunk 20 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:   10.0000
   chunk 18 optimal weight:    9.9990
   chunk 17 optimal weight:    6.9990
   chunk 11 optimal weight:   10.0000
   chunk 29 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 28 optimal weight:    8.9990
   overall best weight:    6.3990

-------------------------------------------------------------------------------
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 = 0.4193 r_free = 0.4193 target = 0.125779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.108292 restraints weight = 2749.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3975 rms_B_bonded: 2.89
r_work: 0.3964 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3954 rms_B_bonded: 2.63 restraints_weight: 0.2500
r_work: 0.3943 rms_B_bonded: 2.63 restraints_weight: 0.1250
r_work: 0.3932 rms_B_bonded: 2.68 restraints_weight: 0.0625
r_work: 0.3921 rms_B_bonded: 2.75 restraints_weight: 0.0312
r_work: 0.3910 rms_B_bonded: 2.84 restraints_weight: 0.0156
r_work: 0.3897 rms_B_bonded: 2.95 restraints_weight: 0.0078
r_work: 0.3884 rms_B_bonded: 3.09 restraints_weight: 0.0039
r_work: 0.3871 rms_B_bonded: 3.24 restraints_weight: 0.0020
r_work: 0.3858 rms_B_bonded: 3.41 restraints_weight: 0.0010
r_work: 0.3843 rms_B_bonded: 3.60 restraints_weight: 0.0005
r_work: 0.3828 rms_B_bonded: 3.82 restraints_weight: 0.0002
r_work: 0.3812 rms_B_bonded: 4.06 restraints_weight: 0.0001
r_work: 0.3795 rms_B_bonded: 4.33 restraints_weight: 0.0001
r_work: 0.3777 rms_B_bonded: 4.62 restraints_weight: 0.0000
r_work: 0.3758 rms_B_bonded: 4.94 restraints_weight: 0.0000
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.3269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.034   2210  Z= 0.394
  Angle     :  0.567   5.176   2985  Z= 0.319
  Chirality :  0.056   0.138    390
  Planarity :  0.002   0.009    375
  Dihedral  :  4.572  14.619    320
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer Outliers :  0.44 %
  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: -2.61 (0.37), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.98 (0.28), residues: 310

===============================================================================
Job complete
usr+sys time: 753.57 seconds
wall clock time: 14 minutes 35.43 seconds (875.43 seconds total)