Starting phenix.real_space_refine
on Wed Aug  5 23:50:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v26_42899/08_2026/8v26_42899_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v26_42899/08_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_42899/08_2026/8v26_42899_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v26_42899/08_2026/8v26_42899_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8v26_42899/08_2026/8v26_42899.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v26_42899/08_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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 1.83, per 1000 atoms: 0.14
  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: 0.93
  Conformation dependent library (CDL) restraints added in 305.8 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: 1.56
  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: 1.87

  Time building geometry restraints manager: 1.15 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 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: 19200
        2.47 -     4.94: 248
        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
     119.70  108.21   11.49 1.20e+00 6.94e-01 9.17e+01
  angle pdb=" C3'  DC I  70 "
        pdb=" O3'  DC I  70 "
        pdb=" P    DG I  71 "
      ideal   model   delta    sigma   weight residual
     119.70  111.30    8.40 1.20e+00 6.94e-01 4.90e+01
  angle pdb=" C3'  DG J  71 "
        pdb=" O3'  DG J  71 "
        pdb=" P    DA J  72 "
      ideal   model   delta    sigma   weight residual
     119.70  113.88    5.82 1.20e+00 6.94e-01 2.36e+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
  ... (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:             1.420
  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:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.400
  Find NCS groups from input model:        0.130
  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:             0.010
  Load rotamer database and sin/cos tables:0.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.140
-------------------------------------------------------------------------------
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     :  0.777  15.432  19468  Z= 0.672
  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       0.76277 /  0.67 (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  : 0.320 
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: 0.1394
  time to fit residues: 23.2104
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  : 0.276 
-------------------------------------------------------------------------------
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...
K  68 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.092553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.060890 restraints weight = 28573.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.2811 rms_B_bonded: 2.07
r_work: 0.2648 rms_B_bonded: 3.53 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 = 0.59   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 = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (11 function evaluations)
r_final: 0.2647
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8879
moved from start:          0.0568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  13499  Z= 0.165
  Angle     :  0.609   7.961  19468  Z= 0.372
  Chirality :  0.046   0.300   2219
  Planarity :  0.004   0.036   1463
  Dihedral  : 29.492 178.693   4116
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 20.48 %
    Favored  : 77.70 %
  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:  2.56 (0.30), residues: 831
  helix:  3.15 (0.22), residues: 537
  sheet: -0.77 (0.86), residues: 26
  loop : -1.25 (0.34), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  96 
 TYR   0.009   0.001   TYR A  54 
 PHE   0.009   0.001   PHE H  67 
 HIS   0.005   0.001   HIS K  68 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.16 (13498)
  covalent geometry    : angle       0.60797 /  0.37 (19466)
  SS BOND              : bond        0.02060 /  1.08 (    1)
  SS BOND              : angle       3.75021 /  2.05 (    2)
  hydrogen bonds       : bond        0.06859 /  4.69 (  772)
  hydrogen bonds       : angle       3.19480 /  2.18 ( 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  : 0.224 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 7
  residues processed: 132
  average time/residue: 0.1306
  time to fit residues: 22.7539
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  : 0.243 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 99 optimal weight:   10.0000
   chunk 48 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   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:    1.7586

-------------------------------------------------------------------------------
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 = 0.3430 r_free = 0.3430 target = 0.092371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.060633 restraints weight = 28643.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.2802 rms_B_bonded: 2.08
r_work: 0.2638 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2638
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2640
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2640 r_free = 0.2640    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2640 r_free = 0.2640    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2640
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8866
moved from start:          0.0789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13499  Z= 0.172
  Angle     :  0.592   7.888  19468  Z= 0.358
  Chirality :  0.044   0.224   2219
  Planarity :  0.004   0.038   1463
  Dihedral  : 29.673 179.179   4116
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 21.18 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.63 (0.30), residues: 831
  helix:  3.19 (0.22), residues: 538
  sheet: -0.54 (0.91), residues: 26
  loop : -1.25 (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   0.010   0.002   PHE H  67 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.17 (13498)
  covalent geometry    : angle       0.59110 /  0.36 (19466)
  SS BOND              : bond        0.00770 /  0.41 (    1)
  SS BOND              : angle       2.35532 /  1.32 (    2)
  hydrogen bonds       : bond        0.06739 /  4.58 (  772)
  hydrogen bonds       : angle       3.10494 /  2.14 ( 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
  142 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
REVERT: H   31 LYS cc_start: 0.9044 (mmtt) cc_final: 0.8413 (mtpt)
REVERT: K    1 MET cc_start: 0.6636 (pmm) cc_final: 0.6154 (pmm)
REVERT: K   42 ARG cc_start: 0.8316 (ttp80) cc_final: 0.7644 (ttp80)
  outliers start: 16
  outliers final: 11
  residues processed: 135
  average time/residue: 0.1347
  time to fit residues: 24.1986
Evaluate side-chains
  134 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 123
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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:    0.7980
   chunk 26 optimal weight:    5.9990
   chunk 69 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 75 optimal weight:   20.0000
   chunk 88 optimal weight:   20.0000
   chunk 54 optimal weight:    8.9990
   chunk 57 optimal weight:    0.3980
   chunk 29 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 = 0.093388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.061697 restraints weight = 28284.330|
|-----------------------------------------------------------------------------|
r_work (start): 0.2828 rms_B_bonded: 2.12
r_work: 0.2660 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2660
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2659
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2659 r_free = 0.2659    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2659 r_free = 0.2659    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2659
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8874
moved from start:          0.0922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  13499  Z= 0.147
  Angle     :  0.569   9.277  19468  Z= 0.346
  Chirality :  0.043   0.226   2219
  Planarity :  0.004   0.036   1463
  Dihedral  : 29.680 178.410   4116
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 21.32 %
    Favored  : 76.30 %
  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:  2.69 (0.30), residues: 831
  helix:  3.24 (0.22), residues: 538
  sheet: -0.51 (0.92), residues: 26
  loop : -1.23 (0.34), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  99 
 TYR   0.008   0.001   TYR H  37 
 PHE   0.008   0.001   PHE E  78 
 HIS   0.002   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00229 /  0.15 (13498)
  covalent geometry    : angle       0.56868 /  0.35 (19466)
  SS BOND              : bond        0.00429 /  0.23 (    1)
  SS BOND              : angle       1.42786 /  0.80 (    2)
  hydrogen bonds       : bond        0.06103 /  4.15 (  772)
  hydrogen bonds       : angle       2.99134 /  2.06 ( 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: 17
    poor density    : 128
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8503 (pm20)
REVERT: F   24 ASP cc_start: 0.7911 (p0) cc_final: 0.7711 (p0)
  outliers start: 17
  outliers final: 14
  residues processed: 136
  average time/residue: 0.1325
  time to fit residues: 23.8009
Evaluate side-chains
  140 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 125
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
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 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   62 ILE
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:    3.9990
   chunk 78 optimal weight:   20.0000
   chunk 9 optimal weight:    0.6980
   chunk 57 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 49 optimal weight:    0.6980
   chunk 105 optimal weight:   30.0000
   chunk 15 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3471 r_free = 0.3471 target = 0.094871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.063586 restraints weight = 28648.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.2866 rms_B_bonded: 2.08
r_work: 0.2707 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2707
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2707 r_free = 0.2707    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2707 r_free = 0.2707    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2707
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8802
moved from start:          0.1203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  13499  Z= 0.139
  Angle     :  0.542   7.571  19468  Z= 0.332
  Chirality :  0.041   0.220   2219
  Planarity :  0.004   0.039   1463
  Dihedral  : 29.748 177.543   4116
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 21.74 %
    Favored  : 75.60 %
  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:  2.89 (0.30), residues: 831
  helix:  3.38 (0.22), residues: 541
  sheet: -0.34 (0.93), residues: 26
  loop : -1.18 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG K  42 
 TYR   0.008   0.001   TYR H  37 
 PHE   0.008   0.001   PHE H  67 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00216 /  0.14 (13498)
  covalent geometry    : angle       0.54190 /  0.33 (19466)
  SS BOND              : bond        0.00519 /  0.27 (    1)
  SS BOND              : angle       1.03341 /  0.58 (    2)
  hydrogen bonds       : bond        0.05339 /  3.62 (  772)
  hydrogen bonds       : angle       2.82877 /  1.94 ( 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
  145 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 126
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8434 (pm20)
REVERT: A   63 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7915 (mmp80)
REVERT: F   24 ASP cc_start: 0.7952 (p0) cc_final: 0.7747 (p0)
REVERT: H   31 LYS cc_start: 0.9025 (mmtt) cc_final: 0.8425 (mtpt)
REVERT: K   42 ARG cc_start: 0.8272 (ttp80) cc_final: 0.7698 (ttp80)
  outliers start: 19
  outliers final: 12
  residues processed: 136
  average time/residue: 0.1316
  time to fit residues: 23.9279
Evaluate side-chains
  136 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
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  110 CYS
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  112 ILE
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain F residue   30 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:   30.0000
   chunk 26 optimal weight:    0.0060
   chunk 72 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 63 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   overall best weight:    1.7202

-------------------------------------------------------------------------------
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 = 0.3448 r_free = 0.3448 target = 0.093441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.061806 restraints weight = 28464.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.2829 rms_B_bonded: 2.07
r_work: 0.2667 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2667
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2667 r_free = 0.2667    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2667 r_free = 0.2667    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2667
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8839
moved from start:          0.1183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13499  Z= 0.165
  Angle     :  0.574   7.791  19468  Z= 0.343
  Chirality :  0.042   0.217   2219
  Planarity :  0.004   0.035   1463
  Dihedral  : 29.809 178.025   4116
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 21.32 %
    Favored  : 75.60 %
  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:  2.83 (0.30), residues: 831
  helix:  3.33 (0.22), residues: 541
  sheet: -0.01 (0.97), residues: 26
  loop : -1.24 (0.34), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  96 
 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        0.00311 /  0.17 (13498)
  covalent geometry    : angle       0.57405 /  0.34 (19466)
  SS BOND              : bond        0.00679 /  0.36 (    1)
  SS BOND              : angle       1.25517 /  0.72 (    2)
  hydrogen bonds       : bond        0.06047 /  4.11 (  772)
  hydrogen bonds       : angle       2.92795 /  2.02 ( 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
  147 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 125
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8485 (pm20)
REVERT: A   63 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7980 (mmp80)
REVERT: F   24 ASP cc_start: 0.7937 (p0) cc_final: 0.7718 (p0)
REVERT: H   31 LYS cc_start: 0.9043 (mmtt) cc_final: 0.8445 (mtpt)
REVERT: K    1 MET cc_start: 0.6650 (pmm) cc_final: 0.6138 (pmm)
REVERT: K   42 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7922 (ptm-80)
  outliers start: 22
  outliers final: 16
  residues processed: 138
  average time/residue: 0.1321
  time to fit residues: 24.2156
Evaluate side-chains
  143 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
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   73 GLU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 101 optimal weight:    9.9990
   chunk 51 optimal weight:    2.9990
   chunk 73 optimal weight:   20.0000
   chunk 13 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 82 optimal weight:   20.0000
   chunk 6 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.094164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.062751 restraints weight = 28487.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.2847 rms_B_bonded: 2.07
r_work: 0.2685 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2685
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2685 r_free = 0.2685    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2685 r_free = 0.2685    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.2685
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8819
moved from start:          0.1258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  13499  Z= 0.144
  Angle     :  0.558   8.653  19468  Z= 0.336
  Chirality :  0.041   0.214   2219
  Planarity :  0.004   0.064   1463
  Dihedral  : 29.802 177.598   4116
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 22.44 %
    Favored  : 74.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.88 (0.30), residues: 831
  helix:  3.37 (0.22), residues: 539
  sheet: -0.07 (0.97), residues: 26
  loop : -1.18 (0.34), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D  27 
 TYR   0.008   0.001   TYR H  37 
 PHE   0.008   0.001   PHE H  67 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00236 /  0.14 (13498)
  covalent geometry    : angle       0.55729 /  0.34 (19466)
  SS BOND              : bond        0.01496 /  0.79 (    1)
  SS BOND              : angle       2.11884 /  1.13 (    2)
  hydrogen bonds       : bond        0.05685 /  3.87 (  772)
  hydrogen bonds       : angle       2.86336 /  1.98 ( 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
  142 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8441 (pm20)
REVERT: A   63 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7965 (mmp80)
REVERT: D   31 LYS cc_start: 0.9186 (mtmm) cc_final: 0.8906 (mtmm)
REVERT: H   31 LYS cc_start: 0.9045 (mmtt) cc_final: 0.8454 (mtpt)
REVERT: K   42 ARG cc_start: 0.8250 (ttp80) cc_final: 0.7903 (ptm-80)
  outliers start: 19
  outliers final: 16
  residues processed: 135
  average time/residue: 0.1219
  time to fit residues: 21.9799
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  : 0.194 
-------------------------------------------------------------------------------
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 D residue   98 LEU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 45 optimal weight:    0.0870
   chunk 9 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 39 optimal weight:    4.9990
   chunk 79 optimal weight:   20.0000
   chunk 107 optimal weight:   40.0000
   chunk 10 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 73 optimal weight:   20.0000
   chunk 102 optimal weight:   30.0000
   overall best weight:    1.3564

-------------------------------------------------------------------------------
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 = 0.3457 r_free = 0.3457 target = 0.093940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.062463 restraints weight = 28281.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.2842 rms_B_bonded: 2.06
r_work: 0.2680 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2681
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2681 r_free = 0.2681    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 = 0.2681 r_free = 0.2681    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (11 function evaluations)
r_final: 0.2681
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8828
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      :  0.003   0.036  13499  Z= 0.152
  Angle     :  0.566   9.019  19468  Z= 0.337
  Chirality :  0.041   0.209   2219
  Planarity :  0.004   0.035   1463
  Dihedral  : 29.837 177.436   4116
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  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:  2.86 (0.30), residues: 831
  helix:  3.36 (0.22), residues: 539
  sheet: -0.05 (0.98), residues: 26
  loop : -1.21 (0.34), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D  27 
 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        0.00268 /  0.15 (13498)
  covalent geometry    : angle       0.56629 /  0.34 (19466)
  SS BOND              : bond        0.01134 /  0.60 (    1)
  SS BOND              : angle       1.49135 /  0.79 (    2)
  hydrogen bonds       : bond        0.05847 /  3.97 (  772)
  hydrogen bonds       : angle       2.88438 /  1.99 ( 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
  143 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8474 (pm20)
REVERT: A   63 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7973 (mmp80)
REVERT: H   31 LYS cc_start: 0.9048 (mmtt) cc_final: 0.8451 (mtpt)
REVERT: K   42 ARG cc_start: 0.8252 (ttp80) cc_final: 0.7900 (ptm-80)
  outliers start: 20
  outliers final: 16
  residues processed: 134
  average time/residue: 0.1330
  time to fit residues: 23.6192
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  : 0.270 
-------------------------------------------------------------------------------
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   73 GLU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 84 optimal weight:   20.0000
   chunk 45 optimal weight:    0.3980
   chunk 60 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   chunk 103 optimal weight:    0.5980
   chunk 37 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 = 0.3461 r_free = 0.3461 target = 0.094191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.062725 restraints weight = 28448.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.2850 rms_B_bonded: 2.06
r_work: 0.2684 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2683
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2683 r_free = 0.2683    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2683 r_free = 0.2683    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (10 function evaluations)
r_final: 0.2683
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8839
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      :  0.002   0.054  13499  Z= 0.143
  Angle     :  0.562   9.632  19468  Z= 0.336
  Chirality :  0.041   0.209   2219
  Planarity :  0.004   0.037   1463
  Dihedral  : 29.840 177.446   4116
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 22.30 %
    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:  2.86 (0.30), residues: 831
  helix:  3.37 (0.22), residues: 539
  sheet: -0.18 (0.96), residues: 26
  loop : -1.20 (0.34), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D  27 
 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        0.00235 /  0.14 (13498)
  covalent geometry    : angle       0.56140 /  0.34 (19466)
  SS BOND              : bond        0.01113 /  0.59 (    1)
  SS BOND              : angle       1.35346 /  0.73 (    2)
  hydrogen bonds       : bond        0.05712 /  3.88 (  772)
  hydrogen bonds       : angle       2.86834 /  1.98 ( 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
  142 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8467 (pm20)
REVERT: A   63 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7980 (mmp80)
REVERT: D   31 LYS cc_start: 0.9201 (mtmm) cc_final: 0.8945 (mtmm)
REVERT: H   31 LYS cc_start: 0.9047 (mmtt) cc_final: 0.8459 (mtpt)
REVERT: K    6 LYS cc_start: 0.9227 (pptt) cc_final: 0.8806 (tptp)
REVERT: K   42 ARG cc_start: 0.8252 (ttp80) cc_final: 0.7888 (ptm-80)
  outliers start: 19
  outliers final: 16
  residues processed: 134
  average time/residue: 0.1358
  time to fit residues: 24.2575
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  : 0.210 
-------------------------------------------------------------------------------
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   73 GLU
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 53 optimal weight:    4.9990
   chunk 97 optimal weight:   10.0000
   chunk 75 optimal weight:   20.0000
   chunk 27 optimal weight:    0.0370
   chunk 42 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   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:    1.8066

-------------------------------------------------------------------------------
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 = 0.3438 r_free = 0.3438 target = 0.092801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.061038 restraints weight = 28584.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.2811 rms_B_bonded: 2.08
r_work: 0.2646 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.2646
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2645
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2645 r_free = 0.2645    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2645 r_free = 0.2645    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2645
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8875
moved from start:          0.1314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13499  Z= 0.168
  Angle     :  0.593  11.078  19468  Z= 0.347
  Chirality :  0.043   0.211   2219
  Planarity :  0.004   0.040   1463
  Dihedral  : 29.923 177.781   4116
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 22.58 %
    Favored  : 74.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  3.28 (0.22), residues: 539
  sheet: -0.01 (1.01), residues: 26
  loop : -1.28 (0.34), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D  27 
 TYR   0.009   0.001   TYR H  39 
 PHE   0.009   0.002   PHE H  67 
 HIS   0.004   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.17 (13498)
  covalent geometry    : angle       0.59287 /  0.35 (19466)
  SS BOND              : bond        0.01158 /  0.61 (    1)
  SS BOND              : angle       1.21010 /  0.65 (    2)
  hydrogen bonds       : bond        0.06504 /  4.41 (  772)
  hydrogen bonds       : angle       2.97571 /  2.06 ( 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
  145 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8438 (pm20)
REVERT: A   63 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8042 (mmp80)
REVERT: H   31 LYS cc_start: 0.9058 (mmtt) cc_final: 0.8478 (mtpt)
REVERT: K   42 ARG cc_start: 0.8300 (ttp80) cc_final: 0.7927 (ptm-80)
  outliers start: 18
  outliers final: 15
  residues processed: 137
  average time/residue: 0.1376
  time to fit residues: 24.8846
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  : 0.314 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 102 optimal weight:   30.0000
   chunk 42 optimal weight:    0.8980
   chunk 60 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 89 optimal weight:   20.0000
   chunk 91 optimal weight:   20.0000
   chunk 107 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   overall best weight:    3.7186

-------------------------------------------------------------------------------
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 = 0.3379 r_free = 0.3379 target = 0.089378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.057336 restraints weight = 28401.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.2730 rms_B_bonded: 2.05
r_work: 0.2553 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2553
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2554
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2554 r_free = 0.2554    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2554 r_free = 0.2554    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2554
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8948
moved from start:          0.1376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063  13499  Z= 0.266
  Angle     :  0.714  14.828  19468  Z= 0.402
  Chirality :  0.050   0.244   2219
  Planarity :  0.005   0.044   1463
  Dihedral  : 30.026 179.749   4116
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 22.86 %
    Favored  : 74.75 %
  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:  2.21 (0.29), residues: 831
  helix:  2.85 (0.22), residues: 538
  sheet: -0.04 (0.99), residues: 26
  loop : -1.44 (0.34), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  96 
 TYR   0.015   0.002   TYR A  54 
 PHE   0.015   0.002   PHE D  67 
 HIS   0.004   0.001   HIS H  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00594 /  0.27 (13498)
  covalent geometry    : angle       0.71382 /  0.40 (19466)
  SS BOND              : bond        0.01666 /  0.88 (    1)
  SS BOND              : angle       1.65066 /  0.90 (    2)
  hydrogen bonds       : bond        0.08898 /  6.03 (  772)
  hydrogen bonds       : angle       3.39719 /  2.38 ( 1947)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2205.60 seconds
wall clock time: 38 minutes 26.71 seconds (2306.71 seconds total)