Starting phenix.real_space_refine
on Fri Jul  3 05:39:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v26_42899/07_2026/8v26_42899_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v26_42899/07_2026/8v26_42899.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.33
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v26_42899/07_2026/8v26_42899_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v26_42899/07_2026/8v26_42899_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8v26_42899/07_2026/8v26_42899.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v26_42899/07_2026/8v26_42899.map"
  }
  resolution = 3.33
  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=   0.002 sd=   0.019
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     288      5.49       5
     S      16      5.16       5
     C    7063      2.51       5
     N    2387      2.21       5
     O    2935      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12689
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 811
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 859
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 859
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 5, 'TRANS': 105}
    Chain: "D"
      Number of atoms: 764
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 764
          Classifications: {'peptide': 97}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 94}
    Chain: "E"
      Number of atoms: 817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 817
          Classifications: {'peptide': 99}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 841
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 841
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 754
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
    Chain: "I"
      Number of atoms: 2952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2952
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2987
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "K"
      Number of atoms: 604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 604
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb=" N   LEU K  73 " occ=0.95
      ... (6 atoms not shown)
      pdb=" CD2 LEU K  73 " occ=0.95
    residue:
      pdb=" N   ARG K  74 " occ=0.77
      ... (9 atoms not shown)
      pdb=" NH2 ARG K  74 " occ=0.77
    residue:
      pdb=" N   GLY K  75 " occ=0.75
      ... (2 atoms not shown)
      pdb=" O   GLY K  75 " occ=0.75
  Time building chain proxies: 2.57, per 1000 atoms: 0.20
  Number of scatterers: 12689
  At special positions: 0
  Unit cell: (100.88, 123.19, 119.31, 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      16     16.00
     P     288     15.00
     O    2935      8.00
     N    2387      7.00
     C    7063      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 117 " - pdb=" SG  CYS K  76 " distance=2.56

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Conformation dependent library (CDL) restraints added in 390.3 milliseconds
  

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1592

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 9 sheets defined
      66.5% alpha, 4.4% beta
      139 base pairs and 249 stacking pairs defined.
    Time for finding SS restraints: 1.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.525A  pdb=" N   SER A  57 " --> pdb=" O   ARG A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.834A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.833A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.651A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
      removed outlier: 3.557A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.196A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.541A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
      removed outlier: 3.548A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.628A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
      removed outlier: 3.665A  pdb=" N   ASN D  81 " --> pdb=" O   LEU D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 3.567A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 121
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 3.517A  pdb=" N   SER E  57 " --> pdb=" O   ARG E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.568A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.786A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.572A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.512A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.230A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.918A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 46 through 73
      removed outlier: 3.502A  pdb=" N   TYR G  50 " --> pdb=" O   GLY G  46 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
      removed outlier: 3.520A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
      removed outlier: 3.723A  pdb=" N   ASN H  81 " --> pdb=" O   LEU H  77 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 121
      removed outlier: 3.591A  pdb=" N   ALA H 121 " --> pdb=" O   CYS H 117 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 22 through 35
    Processing helix  chain 'K' and resid 37 through 39
      No H-bonds generated for 'chain 'K' and resid 37 through 39'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.170A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.389A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.797A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.510A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.357A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'K' and resid 12 through 16
      removed outlier: 4.011A  pdb=" N   SER K  65 " --> pdb=" O   GLN K   2 " (cutoff:3.500A)

    415 hydrogen bonds defined for protein.
    1233 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      357 hydrogen bonds
      714 hydrogen bond angles
      0 basepair planarities
      139 basepair parallelities
      249 stacking parallelities
  Total time for adding SS restraints: 1.83

  Time building geometry restraints manager: 1.38 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2575
        1.33 -     1.45: 4230
        1.45 -     1.57: 6090
        1.57 -     1.69: 576
        1.69 -     1.81: 27
  Bond restraints: 13498
  Sorted by residual:
  bond pdb=" C1'  DG I -70 "
       pdb=" N9   DG I -70 "
    ideal  model  delta    sigma   weight residual
    1.468  1.386  0.082 1.40e-02 5.10e+03 3.41e+01
  bond pdb=" C1'  DT J -72 "
       pdb=" N1   DT J -72 "
    ideal  model  delta    sigma   weight residual
    1.468  1.549 -0.081 1.40e-02 5.10e+03 3.34e+01
  bond pdb=" C1'  DT I -72 "
       pdb=" N1   DT I -72 "
    ideal  model  delta    sigma   weight residual
    1.468  1.547 -0.079 1.40e-02 5.10e+03 3.19e+01
  bond pdb=" C1'  DG J -70 "
       pdb=" N9   DG J -70 "
    ideal  model  delta    sigma   weight residual
    1.468  1.389  0.079 1.40e-02 5.10e+03 3.19e+01
  bond pdb=" C1'  DC I  70 "
       pdb=" N1   DC I  70 "
    ideal  model  delta    sigma   weight residual
    1.468  1.544 -0.076 1.40e-02 5.10e+03 2.92e+01
  ... (remaining 13493 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.47: 19201
        2.47 -     4.94: 247
        4.94 -     7.41: 14
        7.41 -     9.87: 2
        9.87 -    12.34: 2
  Bond angle restraints: 19466
  Sorted by residual:
  angle pdb=" C3'  DG I  71 "
        pdb=" O3'  DG I  71 "
        pdb=" P    DA I  72 "
      ideal   model   delta    sigma   weight residual
     120.20  108.21   11.99 1.50e+00 4.44e-01 6.39e+01
  angle pdb=" C3'  DC I  70 "
        pdb=" O3'  DC I  70 "
        pdb=" P    DG I  71 "
      ideal   model   delta    sigma   weight residual
     120.20  111.30    8.90 1.50e+00 4.44e-01 3.52e+01
  angle pdb=" O4'  DG J  32 "
        pdb=" C4'  DG J  32 "
        pdb=" C3'  DG J  32 "
      ideal   model   delta    sigma   weight residual
     106.00  103.23    2.77 6.00e-01 2.78e+00 2.13e+01
  angle pdb=" N3   DT J   9 "
        pdb=" C4   DT J   9 "
        pdb=" O4   DT J   9 "
      ideal   model   delta    sigma   weight residual
     119.90  122.62   -2.72 6.00e-01 2.78e+00 2.05e+01
  angle pdb=" N3   DT I -42 "
        pdb=" C4   DT I -42 "
        pdb=" O4   DT I -42 "
      ideal   model   delta    sigma   weight residual
     119.90  122.58   -2.68 6.00e-01 2.78e+00 1.99e+01
  ... (remaining 19461 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.92: 6043
       35.92 -    71.83: 1355
       71.83 -   107.75: 8
      107.75 -   143.67: 4
      143.67 -   179.58: 1
  Dihedral angle restraints: 7411
    sinusoidal: 4948
      harmonic: 2463
  Sorted by residual:
  dihedral pdb=" CB  CYS D 117 "
           pdb=" SG  CYS D 117 "
           pdb=" SG  CYS K  76 "
           pdb=" CB  CYS K  76 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   20.45   72.55     1      1.00e+01 1.00e-02 6.72e+01
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   40.42  179.58     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DT J  54 "
           pdb=" C3'  DT J  54 "
           pdb=" O3'  DT J  54 "
           pdb=" P    DC J  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00  100.64  119.36     1      3.50e+01 8.16e-04 1.17e+01
  ... (remaining 7408 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 2147
       0.098 -    0.196: 68
       0.196 -    0.293: 0
       0.293 -    0.391: 0
       0.391 -    0.489: 4
  Chirality restraints: 2219
  Sorted by residual:
  chirality pdb=" P    DG J  71 "
            pdb=" OP1  DG J  71 "
            pdb=" OP2  DG J  71 "
            pdb=" O5'  DG J  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.82   -0.49 2.00e-01 2.50e+01 5.97e+00
  chirality pdb=" P    DG I  71 "
            pdb=" OP1  DG I  71 "
            pdb=" OP2  DG I  71 "
            pdb=" O5'  DG I  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.81   -0.47 2.00e-01 2.50e+01 5.58e+00
  chirality pdb=" P    DA J  72 "
            pdb=" OP1  DA J  72 "
            pdb=" OP2  DA J  72 "
            pdb=" O5'  DA J  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.80   -0.47 2.00e-01 2.50e+01 5.47e+00
  ... (remaining 2216 not shown)

  Planarity restraints: 1463
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP F  24 "    0.011 2.00e-02 2.50e+03   2.22e-02 4.94e+00
        pdb=" CG  ASP F  24 "   -0.038 2.00e-02 2.50e+03
        pdb=" OD1 ASP F  24 "    0.014 2.00e-02 2.50e+03
        pdb=" OD2 ASP F  24 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP F  24 "    0.011 2.00e-02 2.50e+03   2.14e-02 4.59e+00
        pdb=" C   ASP F  24 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   ASP F  24 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ASN F  25 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP B  24 "   -0.010 2.00e-02 2.50e+03   1.98e-02 3.92e+00
        pdb=" CG  ASP B  24 "    0.034 2.00e-02 2.50e+03
        pdb=" OD1 ASP B  24 "   -0.012 2.00e-02 2.50e+03
        pdb=" OD2 ASP B  24 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1460 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2181
        2.78 -     3.31: 10455
        3.31 -     3.84: 22518
        3.84 -     4.37: 26520
        4.37 -     4.90: 38861
  Nonbonded interactions: 100535
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN K  40 "
            pdb=" NE2 GLN K  41 "
     model   vdw
     2.255 3.120
  nonbonded pdb=" NH1 ARG K  42 "
            pdb=" OE1 GLN K  49 "
     model   vdw
     2.259 3.120
  nonbonded pdb=" O   THR E  58 "
            pdb=" OG1 THR E  58 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" N   MET K   1 "
            pdb=" O   VAL K  17 "
     model   vdw
     2.278 3.120
  nonbonded pdb=" OE1 GLU E  73 "
            pdb=" ND2 ASN F  25 "
     model   vdw
     2.320 3.120
  ... (remaining 100530 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'E' and resid 37 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 23 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 10 through 118)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 26 through 121)
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.59 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.690
  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:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.500
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8883
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      :  0.008   0.527  13499  Z= 0.582
  Angle     :  0.770  15.432  19468  Z= 0.663
  Chirality :  0.048   0.489   2219
  Planarity :  0.004   0.038   1463
  Dihedral  : 27.205 179.584   5816
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 20.76 %
    Favored  : 78.96 %
  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:  2.29 (0.29), residues: 831
  helix:  3.00 (0.22), residues: 525
  sheet: -0.73 (0.98), residues: 26
  loop : -1.31 (0.34), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  96 
 TYR   0.013   0.001   TYR H  39 
 PHE   0.008   0.001   PHE H  67 
 HIS   0.003   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00597 /  0.54 (13498)
  covalent geometry    : angle       0.75641 /  0.66 (19466)
  SS BOND              : bond        0.52747 / 27.76 (    1)
  SS BOND              : angle      14.42575 /  7.99 (    2)
  hydrogen bonds       : bond        0.11579 /  8.01 (  772)
  hydrogen bonds       : angle       3.63269 /  2.52 ( 1947)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 126
  time to evaluate  : 0.287 
Fit side-chains
REVERT: K    6 LYS cc_start: 0.9172 (pttt) cc_final: 0.8944 (tptp)
REVERT: K   68 HIS cc_start: 0.8962 (m170) cc_final: 0.8598 (m90)
  outliers start: 2
  outliers final: 1
  residues processed: 126
  average time/residue: 0.1519
  time to fit residues: 25.1609
Evaluate side-chains
  125 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   36 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:   20.0000
   chunk 106 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  85 GLN
K  68 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.092454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.060862 restraints weight = 28574.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.2807 rms_B_bonded: 2.08
r_work: 0.2644 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2644
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2645
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2645 r_free = 0.2645    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2644 r_free = 0.2644    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (11 function evaluations)
r_final: 0.2644
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8865
moved from start:          0.0553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074  13499  Z= 0.169
  Angle     :  0.603   7.899  19468  Z= 0.371
  Chirality :  0.045   0.281   2219
  Planarity :  0.004   0.036   1463
  Dihedral  : 29.499 178.263   4116
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 20.62 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.57 (0.30), residues: 831
  helix:  3.15 (0.22), residues: 537
  sheet: -0.78 (0.86), residues: 26
  loop : -1.25 (0.34), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  96 
 TYR   0.008   0.001   TYR A  54 
 PHE   0.009   0.001   PHE H  67 
 HIS   0.006   0.001   HIS K  68 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.17 (13498)
  covalent geometry    : angle       0.60110 /  0.37 (19466)
  SS BOND              : bond        0.02086 /  1.10 (    1)
  SS BOND              : angle       4.12906 /  2.25 (    2)
  hydrogen bonds       : bond        0.06887 /  4.71 (  772)
  hydrogen bonds       : angle       3.20305 /  2.19 ( 1947)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 126
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 7
  residues processed: 132
  average time/residue: 0.1321
  time to fit residues: 23.4095
Evaluate side-chains
  130 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 123
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   98 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 99 optimal weight:   20.0000
   chunk 48 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 73 optimal weight:   30.0000
   chunk 78 optimal weight:   20.0000
   chunk 74 optimal weight:   20.0000
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.5384

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.092735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.060916 restraints weight = 28677.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.2812 rms_B_bonded: 2.10
r_work: 0.2648 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2648
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2647
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2647 r_free = 0.2647    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2647 r_free = 0.2647    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2647
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8856
moved from start:          0.0799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13499  Z= 0.165
  Angle     :  0.573   7.326  19468  Z= 0.351
  Chirality :  0.043   0.213   2219
  Planarity :  0.004   0.037   1463
  Dihedral  : 29.698 178.822   4116
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 21.32 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.67 (0.30), residues: 831
  helix:  3.22 (0.22), residues: 538
  sheet: -0.50 (0.92), residues: 26
  loop : -1.24 (0.34), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K  42 
 TYR   0.009   0.001   TYR A  54 
 PHE   0.009   0.001   PHE H  67 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.16 (13498)
  covalent geometry    : angle       0.57237 /  0.35 (19466)
  SS BOND              : bond        0.00842 /  0.44 (    1)
  SS BOND              : angle       2.27283 /  1.29 (    2)
  hydrogen bonds       : bond        0.06495 /  4.41 (  772)
  hydrogen bonds       : angle       3.06831 /  2.11 ( 1947)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
REVERT: H   31 LYS cc_start: 0.9039 (mmtt) cc_final: 0.8409 (mtpt)
REVERT: K    1 MET cc_start: 0.6672 (pmm) cc_final: 0.6190 (pmm)
REVERT: K   42 ARG cc_start: 0.8313 (ttp80) cc_final: 0.7632 (ttp80)
  outliers start: 14
  outliers final: 10
  residues processed: 132
  average time/residue: 0.1532
  time to fit residues: 26.8152
Evaluate side-chains
  133 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 123
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain K residue    3 ILE
Chi-restraints excluded: chain K residue   44 ILE
Chi-restraints excluded: chain K residue   68 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   chunk 26 optimal weight:    5.9990
   chunk 69 optimal weight:    3.9990
   chunk 7 optimal weight:    5.9990
   chunk 75 optimal weight:   20.0000
   chunk 88 optimal weight:   20.0000
   chunk 54 optimal weight:   10.0000
   chunk 57 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   overall best weight:    1.7384

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.092546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.060919 restraints weight = 28346.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.2805 rms_B_bonded: 2.07
r_work: 0.2641 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2641
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2642
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2642 r_free = 0.2642    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2642 r_free = 0.2642    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2642
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8860
moved from start:          0.0963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  13499  Z= 0.168
  Angle     :  0.574   7.501  19468  Z= 0.348
  Chirality :  0.043   0.213   2219
  Planarity :  0.004   0.037   1463
  Dihedral  : 29.810 178.465   4116
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 21.46 %
    Favored  : 76.02 %
  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:  2.66 (0.30), residues: 831
  helix:  3.18 (0.22), residues: 541
  sheet: -0.28 (0.94), residues: 26
  loop : -1.25 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  99 
 TYR   0.009   0.001   TYR A  54 
 PHE   0.010   0.002   PHE H  67 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.17 (13498)
  covalent geometry    : angle       0.57423 /  0.35 (19466)
  SS BOND              : bond        0.00911 /  0.48 (    1)
  SS BOND              : angle       1.64289 /  0.93 (    2)
  hydrogen bonds       : bond        0.06527 /  4.43 (  772)
  hydrogen bonds       : angle       3.04452 /  2.10 ( 1947)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8469 (pm20)
REVERT: A   63 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8045 (mmp80)
REVERT: F   24 ASP cc_start: 0.7971 (p0) cc_final: 0.7765 (p0)
REVERT: H   31 LYS cc_start: 0.9041 (mmtt) cc_final: 0.8437 (mtpt)
  outliers start: 18
  outliers final: 13
  residues processed: 138
  average time/residue: 0.1504
  time to fit residues: 27.2528
Evaluate side-chains
  138 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   63 ARG
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain K residue    3 ILE
Chi-restraints excluded: chain K residue   44 ILE
Chi-restraints excluded: chain K residue   68 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 94 optimal weight:   20.0000
   chunk 44 optimal weight:    0.9980
   chunk 78 optimal weight:   20.0000
   chunk 9 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 105 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.8982

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.093579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.062019 restraints weight = 28595.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.2830 rms_B_bonded: 2.09
r_work: 0.2668 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.2668
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2668
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2668 r_free = 0.2668    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2668 r_free = 0.2668    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2668
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8836
moved from start:          0.1055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  13499  Z= 0.145
  Angle     :  0.558   8.201  19468  Z= 0.340
  Chirality :  0.042   0.209   2219
  Planarity :  0.004   0.043   1463
  Dihedral  : 29.812 178.220   4116
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 22.02 %
    Favored  : 75.18 %
  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:  2.74 (0.30), residues: 831
  helix:  3.28 (0.22), residues: 538
  sheet: -0.27 (0.96), residues: 26
  loop : -1.24 (0.34), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG K  42 
 TYR   0.007   0.001   TYR H  37 
 PHE   0.008   0.001   PHE H  67 
 HIS   0.002   0.001   HIS E  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00227 /  0.14 (13498)
  covalent geometry    : angle       0.55789 /  0.34 (19466)
  SS BOND              : bond        0.00501 /  0.26 (    1)
  SS BOND              : angle       1.10200 /  0.62 (    2)
  hydrogen bonds       : bond        0.05980 /  4.07 (  772)
  hydrogen bonds       : angle       2.93503 /  2.02 ( 1947)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 130
  time to evaluate  : 0.359 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8413 (pm20)
REVERT: A   63 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7969 (mmp80)
REVERT: F   24 ASP cc_start: 0.7924 (p0) cc_final: 0.7717 (p0)
REVERT: H   31 LYS cc_start: 0.9040 (mmtt) cc_final: 0.8437 (mtpt)
REVERT: K    1 MET cc_start: 0.6577 (pmm) cc_final: 0.6140 (pmm)
  outliers start: 20
  outliers final: 15
  residues processed: 143
  average time/residue: 0.1472
  time to fit residues: 27.7378
Evaluate side-chains
  143 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   63 ARG
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain K residue    3 ILE
Chi-restraints excluded: chain K residue   44 ILE
Chi-restraints excluded: chain K residue   68 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 105 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.5986

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.092956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.061366 restraints weight = 28420.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.2817 rms_B_bonded: 2.08
r_work: 0.2654 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2654
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2654 r_free = 0.2654    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2654 r_free = 0.2654    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2654
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8846
moved from start:          0.1130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13499  Z= 0.161
  Angle     :  0.566   8.437  19468  Z= 0.342
  Chirality :  0.042   0.208   2219
  Planarity :  0.004   0.042   1463
  Dihedral  : 29.856 178.405   4116
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 21.46 %
    Favored  : 75.32 %
  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:  2.75 (0.30), residues: 831
  helix:  3.26 (0.22), residues: 541
  sheet: -0.23 (1.01), residues: 26
  loop : -1.24 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K  42 
 TYR   0.008   0.001   TYR A  54 
 PHE   0.009   0.001   PHE H  67 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.16 (13498)
  covalent geometry    : angle       0.56604 /  0.34 (19466)
  SS BOND              : bond        0.00621 /  0.33 (    1)
  SS BOND              : angle       1.21214 /  0.70 (    2)
  hydrogen bonds       : bond        0.06219 /  4.22 (  772)
  hydrogen bonds       : angle       2.96646 /  2.05 ( 1947)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 0.386 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8437 (pm20)
REVERT: A   63 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7985 (mmp80)
REVERT: F   24 ASP cc_start: 0.7928 (p0) cc_final: 0.7709 (p0)
REVERT: H   31 LYS cc_start: 0.9047 (mmtt) cc_final: 0.8458 (mtpt)
REVERT: K   42 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7426 (ttp80)
  outliers start: 23
  outliers final: 16
  residues processed: 142
  average time/residue: 0.1426
  time to fit residues: 26.8926
Evaluate side-chains
  144 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   63 ARG
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain K residue    3 ILE
Chi-restraints excluded: chain K residue   44 ILE
Chi-restraints excluded: chain K residue   68 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 101 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 73 optimal weight:   30.0000
   chunk 13 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 49 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 82 optimal weight:   20.0000
   chunk 6 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K  68 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.093775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.062279 restraints weight = 28436.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.2837 rms_B_bonded: 2.08
r_work: 0.2675 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2676
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2676 r_free = 0.2676    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2676 r_free = 0.2676    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (12 function evaluations)
r_final: 0.2676
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8829
moved from start:          0.1234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  13499  Z= 0.146
  Angle     :  0.552   8.172  19468  Z= 0.335
  Chirality :  0.041   0.205   2219
  Planarity :  0.004   0.035   1463
  Dihedral  : 29.858 177.975   4116
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 22.16 %
    Favored  : 75.04 %
  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:  2.80 (0.30), residues: 831
  helix:  3.32 (0.22), residues: 541
  sheet: -0.62 (0.97), residues: 26
  loop : -1.21 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K  42 
 TYR   0.008   0.001   TYR H  37 
 PHE   0.008   0.001   PHE H  67 
 HIS   0.008   0.001   HIS K  68 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00243 /  0.15 (13498)
  covalent geometry    : angle       0.55144 /  0.33 (19466)
  SS BOND              : bond        0.01801 /  0.95 (    1)
  SS BOND              : angle       3.25058 /  1.72 (    2)
  hydrogen bonds       : bond        0.05790 /  3.93 (  772)
  hydrogen bonds       : angle       2.89107 /  2.00 ( 1947)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 128
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8397 (pm20)
REVERT: A   63 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7976 (mmp80)
REVERT: D   31 LYS cc_start: 0.9190 (mtmm) cc_final: 0.8907 (mtmm)
REVERT: F   24 ASP cc_start: 0.7914 (p0) cc_final: 0.7705 (p0)
REVERT: H   31 LYS cc_start: 0.9054 (mmtt) cc_final: 0.8471 (mtpt)
  outliers start: 20
  outliers final: 15
  residues processed: 140
  average time/residue: 0.1273
  time to fit residues: 23.7574
Evaluate side-chains
  143 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   63 ARG
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain K residue    3 ILE
Chi-restraints excluded: chain K residue   44 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 45 optimal weight:    0.0980
   chunk 9 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 79 optimal weight:   20.0000
   chunk 107 optimal weight:   40.0000
   chunk 10 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 67 optimal weight:    2.9990
   chunk 73 optimal weight:   30.0000
   chunk 102 optimal weight:    6.9990
   overall best weight:    1.5986

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.093152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.061572 restraints weight = 28251.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.2822 rms_B_bonded: 2.07
r_work: 0.2660 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2660
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2660
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2660 r_free = 0.2660    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2660 r_free = 0.2660    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2660
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8844
moved from start:          0.1262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13499  Z= 0.162
  Angle     :  0.565   9.218  19468  Z= 0.340
  Chirality :  0.042   0.203   2219
  Planarity :  0.004   0.035   1463
  Dihedral  : 29.907 178.024   4116
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 23.70 %
    Favored  : 73.77 %
  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:  2.78 (0.30), residues: 831
  helix:  3.33 (0.22), residues: 539
  sheet: -0.75 (0.95), residues: 26
  loop : -1.22 (0.35), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG K  42 
 TYR   0.008   0.001   TYR A  54 
 PHE   0.009   0.001   PHE H  67 
 HIS   0.003   0.001   HIS K  68 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.16 (13498)
  covalent geometry    : angle       0.56521 /  0.34 (19466)
  SS BOND              : bond        0.01337 /  0.70 (    1)
  SS BOND              : angle       1.74548 /  0.92 (    2)
  hydrogen bonds       : bond        0.06133 /  4.17 (  772)
  hydrogen bonds       : angle       2.94705 /  2.04 ( 1947)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8422 (pm20)
REVERT: A   63 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7995 (mmp80)
REVERT: F   24 ASP cc_start: 0.7914 (p0) cc_final: 0.7702 (p0)
REVERT: H   31 LYS cc_start: 0.9058 (mmtt) cc_final: 0.8472 (mtpt)
REVERT: K   42 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7007 (ttp80)
  outliers start: 18
  outliers final: 14
  residues processed: 140
  average time/residue: 0.1573
  time to fit residues: 28.9898
Evaluate side-chains
  142 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   63 ARG
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain K residue    3 ILE
Chi-restraints excluded: chain K residue   44 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 84 optimal weight:   20.0000
   chunk 45 optimal weight:    0.0670
   chunk 60 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 103 optimal weight:    0.0270
   chunk 37 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 59 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.5176

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.094115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.062810 restraints weight = 28403.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 2.07
r_work: 0.2682 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2682
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2682 r_free = 0.2682    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2682 r_free = 0.2682    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2682
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8834
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  13499  Z= 0.140
  Angle     :  0.549   9.131  19468  Z= 0.333
  Chirality :  0.041   0.201   2219
  Planarity :  0.004   0.035   1463
  Dihedral  : 29.897 177.908   4116
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 23.56 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.81 (0.30), residues: 831
  helix:  3.34 (0.22), residues: 539
  sheet: -0.79 (0.95), residues: 26
  loop : -1.19 (0.35), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  27 
 TYR   0.008   0.001   TYR H  37 
 PHE   0.009   0.001   PHE H  67 
 HIS   0.002   0.000   HIS E  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00213 /  0.14 (13498)
  covalent geometry    : angle       0.54915 /  0.33 (19466)
  SS BOND              : bond        0.00991 /  0.52 (    1)
  SS BOND              : angle       1.28410 /  0.68 (    2)
  hydrogen bonds       : bond        0.05704 /  3.89 (  772)
  hydrogen bonds       : angle       2.85487 /  1.97 ( 1947)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8404 (pm20)
REVERT: A   63 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7991 (mmp80)
REVERT: D   31 LYS cc_start: 0.9202 (mtmm) cc_final: 0.8934 (mtmm)
REVERT: F   24 ASP cc_start: 0.7904 (p0) cc_final: 0.7699 (p0)
REVERT: H   31 LYS cc_start: 0.9053 (mmtt) cc_final: 0.8469 (mtpt)
  outliers start: 20
  outliers final: 16
  residues processed: 136
  average time/residue: 0.1370
  time to fit residues: 24.6310
Evaluate side-chains
  141 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   63 ARG
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain K residue    3 ILE
Chi-restraints excluded: chain K residue   44 ILE
Chi-restraints excluded: chain K residue   68 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 97 optimal weight:   20.0000
   chunk 75 optimal weight:   10.0000
   chunk 27 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 28 optimal weight:    8.9990
   chunk 15 optimal weight:    1.9990
   chunk 85 optimal weight:   20.0000
   chunk 35 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    1.5990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.093268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.061613 restraints weight = 28632.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.2826 rms_B_bonded: 2.09
r_work: 0.2658 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2658
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2657
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2657 r_free = 0.2657    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2657 r_free = 0.2657    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2657
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8853
moved from start:          0.1333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13499  Z= 0.157
  Angle     :  0.564  10.232  19468  Z= 0.337
  Chirality :  0.042   0.201   2219
  Planarity :  0.004   0.035   1463
  Dihedral  : 29.948 177.853   4116
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 24.12 %
    Favored  : 73.49 %
  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:  2.78 (0.30), residues: 831
  helix:  3.33 (0.22), residues: 539
  sheet: -0.56 (0.95), residues: 26
  loop : -1.25 (0.34), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG K  42 
 TYR   0.008   0.001   TYR H  39 
 PHE   0.009   0.001   PHE H  67 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.16 (13498)
  covalent geometry    : angle       0.56373 /  0.34 (19466)
  SS BOND              : bond        0.01104 /  0.58 (    1)
  SS BOND              : angle       1.21281 /  0.65 (    2)
  hydrogen bonds       : bond        0.06137 /  4.17 (  772)
  hydrogen bonds       : angle       2.92512 /  2.02 ( 1947)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 0.285 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8434 (pm20)
REVERT: A   63 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8016 (mmp80)
REVERT: F   24 ASP cc_start: 0.7928 (p0) cc_final: 0.7713 (p0)
REVERT: H   31 LYS cc_start: 0.9065 (mmtt) cc_final: 0.8480 (mtpt)
  outliers start: 17
  outliers final: 15
  residues processed: 137
  average time/residue: 0.1362
  time to fit residues: 24.6657
Evaluate side-chains
  142 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   63 ARG
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain K residue    3 ILE
Chi-restraints excluded: chain K residue   44 ILE
Chi-restraints excluded: chain K residue   68 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 97 optimal weight:   20.0000
   chunk 48 optimal weight:    0.9980
   chunk 102 optimal weight:   30.0000
   chunk 42 optimal weight:    0.9980
   chunk 60 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   chunk 89 optimal weight:   10.0000
   chunk 91 optimal weight:   20.0000
   chunk 107 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    2.9986

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.090666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.058652 restraints weight = 28465.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.2757 rms_B_bonded: 2.07
r_work: 0.2587 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2587
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2587
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2587 r_free = 0.2587    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2587 r_free = 0.2587    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.2587
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8916
moved from start:          0.1324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  13499  Z= 0.218
  Angle     :  0.651  13.191  19468  Z= 0.374
  Chirality :  0.046   0.212   2219
  Planarity :  0.005   0.036   1463
  Dihedral  : 30.054 179.022   4116
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 23.98 %
    Favored  : 73.49 %
  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:  2.45 (0.29), residues: 831
  helix:  3.07 (0.22), residues: 538
  sheet: -0.68 (0.96), residues: 26
  loop : -1.35 (0.34), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG K  42 
 TYR   0.012   0.001   TYR H  39 
 PHE   0.013   0.002   PHE D  67 
 HIS   0.003   0.001   HIS K  68 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00463 /  0.22 (13498)
  covalent geometry    : angle       0.65083 /  0.37 (19466)
  SS BOND              : bond        0.01462 /  0.77 (    1)
  SS BOND              : angle       1.53996 /  0.83 (    2)
  hydrogen bonds       : bond        0.07880 /  5.34 (  772)
  hydrogen bonds       : angle       3.22046 /  2.23 ( 1947)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2222.29 seconds
wall clock time: 38 minutes 46.82 seconds (2326.82 seconds total)