Starting phenix.real_space_refine
on Wed Feb  4 16:58:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9d3o_46542/02_2026/9d3o_46542.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9d3o_46542/02_2026/9d3o_46542.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9d3o_46542/02_2026/9d3o_46542.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9d3o_46542/02_2026/9d3o_46542.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9d3o_46542/02_2026/9d3o_46542.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9d3o_46542/02_2026/9d3o_46542.map"
  }
  resolution = 3.0
  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=   0.001 sd=   0.052
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     290      5.49       5
     S      14      5.16       5
     C    6651      2.51       5
     N    2274      2.21       5
     O    2808      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12037
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 652
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 652
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "D"
      Number of atoms: 750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 750
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "H"
      Number of atoms: 736
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 730
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 93, 730
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          bond proxies already assigned to first conformer: 734
    Chain: "I"
      Number of atoms: 2978
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2978
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2967
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "C"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "G"
      Number of atoms: 831
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 831
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
  Time building chain proxies: 2.81, per 1000 atoms: 0.23
  Number of scatterers: 12037
  At special positions: 0
  Unit cell: (118.745, 84.15, 117.81, 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      14     16.00
     P     290     15.00
     O    2808      8.00
     N    2274      7.00
     C    6651      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.68
  Conformation dependent library (CDL) restraints added in 243.4 milliseconds
  

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1432

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 10 sheets defined
      70.9% alpha, 3.1% beta
      140 base pairs and 251 stacking pairs defined.
    Time for finding SS restraints: 1.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 56
    Processing helix  chain 'A' and resid 63 through 75
    Processing helix  chain 'A' and resid 76 through 78
      No H-bonds generated for 'chain 'A' and resid 76 through 78'
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.756A  pdb=" N   ALA A  98 " --> pdb=" O   GLU A  94 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ASP A 106 " --> pdb=" O   GLY A 102 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   LEU A 109 " --> pdb=" O   GLU A 105 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 25 through 29
      removed outlier: 3.617A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.935A  pdb=" N   VAL B  70 " --> pdb=" O   ILE B  66 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   TYR B  72 " --> pdb=" O   ASP B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'D' and resid 39 through 49
      removed outlier: 3.502A  pdb=" N   LYS D  43 " --> pdb=" O   VAL D  39 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.536A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 3.760A  pdb=" N   LEU E  48 " --> pdb=" O   GLY E  44 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 4.055A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.710A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   GLY F  56 " --> pdb=" O   GLU F  52 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.555A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 35 through 47
      removed outlier: 3.747A  pdb=" N   TYR H  40 " --> pdb=" O   SER H  36 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   LYS H  41 " --> pdb=" O   VAL H  37 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LYS H  44 " --> pdb=" O   TYR H  40 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   GLN H  45 " --> pdb=" O   LYS H  41 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 53 through 82
    Processing helix  chain 'H' and resid 88 through 100
      removed outlier: 3.531A  pdb=" N   ILE H  92 " --> pdb=" O   THR H  88 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   THR H  94 " --> pdb=" O   ARG H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 101 through 121
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 46 through 72
      removed outlier: 3.639A  pdb=" N   GLU C  56 " --> pdb=" O   ALA C  52 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
      removed outlier: 3.698A  pdb=" N   LEU C  96 " --> pdb=" O   GLU C  92 " (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: 3.821A  pdb=" N   GLU G  56 " --> pdb=" O   ALA G  52 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   LEU G  65 " --> pdb=" O   GLU G  61 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
      removed outlier: 3.782A  pdb=" N   LEU G 116 " --> pdb=" O   ALA G 113 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.171A  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 96 through 98
      removed outlier: 6.873A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54
      removed outlier: 7.321A  pdb=" N   GLY D  53 " --> pdb=" O   ILE C  78 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.904A  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
    Processing sheet with id=AA8, first strand: chain 'F' and resid 96 through 98
    Processing sheet with id=AA9, first strand: chain 'H' and resid 51 through 52
      removed outlier: 7.014A  pdb=" N   GLY H  51 " --> pdb=" O   ILE G  78 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'H' and resid 86 through 87

    386 hydrogen bonds defined for protein.
    1151 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      364 hydrogen bonds
      728 hydrogen bond angles
      0 basepair planarities
      140 basepair parallelities
      251 stacking parallelities
  Total time for adding SS restraints: 2.17

  Time building geometry restraints manager: 0.89 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: 2438
        1.33 -     1.45: 3983
        1.45 -     1.57: 5816
        1.57 -     1.69: 578
        1.69 -     1.81: 26
  Bond restraints: 12841
  Sorted by residual:
  bond pdb=" CG1 ILE D  69 "
       pdb=" CD1 ILE D  69 "
    ideal  model  delta    sigma   weight residual
    1.513  1.427  0.086 3.90e-02 6.57e+02 4.87e+00
  bond pdb=" CA  THR B  54 "
       pdb=" C   THR B  54 "
    ideal  model  delta    sigma   weight residual
    1.523  1.506  0.018 1.30e-02 5.92e+03 1.85e+00
  bond pdb=" C   ALA E  75 "
       pdb=" O   ALA E  75 "
    ideal  model  delta    sigma   weight residual
    1.236  1.253 -0.017 1.29e-02 6.01e+03 1.81e+00
  bond pdb=" C3'  DA J -17 "
       pdb=" O3'  DA J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.454 -0.032 3.00e-02 1.11e+03 1.15e+00
  bond pdb=" C3'  DG J  21 "
       pdb=" C2'  DG J  21 "
    ideal  model  delta    sigma   weight residual
    1.525  1.544 -0.019 2.00e-02 2.50e+03 8.97e-01
  ... (remaining 12836 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.54: 18492
        2.54 -     5.08: 79
        5.08 -     7.63: 2
        7.63 -    10.17: 1
       10.17 -    12.71: 1
  Bond angle restraints: 18575
  Sorted by residual:
  angle pdb=" C   LEU D 101 "
        pdb=" N   LEU D 102 "
        pdb=" CA  LEU D 102 "
      ideal   model   delta    sigma   weight residual
     123.15  110.44   12.71 2.23e+00 2.01e-01 3.25e+01
  angle pdb=" C   GLU B  53 "
        pdb=" N   THR B  54 "
        pdb=" CA  THR B  54 "
      ideal   model   delta    sigma   weight residual
     120.28  125.34   -5.06 1.34e+00 5.57e-01 1.43e+01
  angle pdb=" N   VAL H  42 "
        pdb=" CA  VAL H  42 "
        pdb=" C   VAL H  42 "
      ideal   model   delta    sigma   weight residual
     112.35  107.69    4.66 1.41e+00 5.03e-01 1.09e+01
  angle pdb=" N   VAL B  65 "
        pdb=" CA  VAL B  65 "
        pdb=" C   VAL B  65 "
      ideal   model   delta    sigma   weight residual
     110.53  113.52   -2.99 9.40e-01 1.13e+00 1.01e+01
  angle pdb=" N   GLY B  28 "
        pdb=" CA  GLY B  28 "
        pdb=" C   GLY B  28 "
      ideal   model   delta    sigma   weight residual
     114.16  110.35    3.81 1.21e+00 6.83e-01 9.92e+00
  ... (remaining 18570 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.15: 5496
       35.15 -    70.30: 1444
       70.30 -   105.45: 25
      105.45 -   140.60: 0
      140.60 -   175.75: 2
  Dihedral angle restraints: 6967
    sinusoidal: 4744
      harmonic: 2223
  Sorted by residual:
  dihedral pdb=" C4'  DA J -17 "
           pdb=" C3'  DA J -17 "
           pdb=" O3'  DA J -17 "
           pdb=" P    DG J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   35.75 -175.75     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   72.43  147.57     1      3.50e+01 8.16e-04 1.45e+01
  dihedral pdb=" CA  ASN G  38 "
           pdb=" CB  ASN G  38 "
           pdb=" CG  ASN G  38 "
           pdb=" OD1 ASN G  38 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -169.48  -70.52     2      2.00e+01 2.50e-03 1.07e+01
  ... (remaining 6964 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1298
       0.027 -    0.053: 589
       0.053 -    0.080: 153
       0.080 -    0.107: 50
       0.107 -    0.133: 18
  Chirality restraints: 2108
  Sorted by residual:
  chirality pdb=" CA  ILE F  46 "
            pdb=" N   ILE F  46 "
            pdb=" C   ILE F  46 "
            pdb=" CB  ILE F  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.45e-01
  chirality pdb=" CA  ILE F  29 "
            pdb=" N   ILE F  29 "
            pdb=" C   ILE F  29 "
            pdb=" CB  ILE F  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.38e-01
  chirality pdb=" CA  ILE D  89 "
            pdb=" N   ILE D  89 "
            pdb=" C   ILE D  89 "
            pdb=" CB  ILE D  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.02e-01
  ... (remaining 2105 not shown)

  Planarity restraints: 1346
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 102 "   -0.043 5.00e-02 4.00e+02   6.51e-02 6.79e+00
        pdb=" N   PRO D 103 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO D 103 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO D 103 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE G  79 "   -0.038 5.00e-02 4.00e+02   5.73e-02 5.26e+00
        pdb=" N   PRO G  80 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO G  80 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO G  80 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP F  24 "   -0.010 2.00e-02 2.50e+03   2.00e-02 3.98e+00
        pdb=" C   ASP F  24 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ASP F  24 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ASN F  25 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1343 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1844
        2.77 -     3.30: 10302
        3.30 -     3.83: 23637
        3.83 -     4.37: 28133
        4.37 -     4.90: 40446
  Nonbonded interactions: 104362
  Sorted by model distance:
  nonbonded pdb=" O   LEU G  55 "
            pdb=" OG1 THR G  59 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OH  TYR A  99 "
            pdb=" OE1 GLU A 133 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OG1 THR H  88 "
            pdb=" OE1 GLU H  91 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" NH2 ARG E  53 "
            pdb=" OP1  DT I -65 "
     model   vdw
     2.298 3.120
  nonbonded pdb=" NH1 ARG A  72 "
            pdb=" OP1  DC I -23 "
     model   vdw
     2.302 3.120
  ... (remaining 104357 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'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ 
e C or name O ))))
}
ncs_group {
  reference = (chain 'C' and resid 11 through 118)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and (resid 31 through 107 or resid 109 through 123))
  selection = (chain 'H' and (resid 29 through 105 or resid 107 through 121))
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.540
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     11.880
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
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      :  0.004   0.086  12841  Z= 0.169
  Angle     :  0.620  12.708  18575  Z= 0.395
  Chirality :  0.034   0.133   2108
  Planarity :  0.005   0.065   1346
  Dihedral  : 28.617 175.748   5535
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 20.69 %
    Favored  : 79.31 %
  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:  0.20 (0.30), residues: 752
  helix:  0.73 (0.23), residues: 532
  sheet:  None (None), residues: 0
  loop : -1.21 (0.37), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  45 
 TYR   0.031   0.002   TYR H  40 
 PHE   0.012   0.002   PHE B  61 
 HIS   0.006   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (12841)
  covalent geometry    : angle       0.62014 (18575)
  hydrogen bonds       : bond        0.13028 (  750)
  hydrogen bonds       : angle       4.90339 ( 1879)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.304 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.7782 (tpp80) cc_final: 0.7547 (tpp80)
REVERT: E   42 ARG cc_start: 0.7875 (mmt90) cc_final: 0.6606 (mmm160)
REVERT: E  120 MET cc_start: 0.9097 (mtt) cc_final: 0.8842 (mtt)
REVERT: F   95 ARG cc_start: 0.8194 (mtt-85) cc_final: 0.7972 (mtt-85)
REVERT: G   51 MET cc_start: 0.8890 (tpp) cc_final: 0.8638 (ttt)
REVERT: G   74 LYS cc_start: 0.8570 (mmtt) cc_final: 0.8218 (mppt)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.7773
  time to fit residues: 79.0113
Evaluate side-chains
  85 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:   30.0000
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
D  84 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.192210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.124927 restraints weight = 28694.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 2.21
r_work: 0.3287 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3298
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3298 r_free = 0.3298    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3298 r_free = 0.3298    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3298
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.1031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057  12841  Z= 0.255
  Angle     :  0.642   6.044  18575  Z= 0.377
  Chirality :  0.039   0.147   2108
  Planarity :  0.006   0.057   1346
  Dihedral  : 31.084 173.741   4001
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 20.38 %
    Favored  : 75.71 %
  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:  0.54 (0.30), residues: 752
  helix:  1.03 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.34 (0.37), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  72 
 TYR   0.014   0.002   TYR C  57 
 PHE   0.016   0.002   PHE B  61 
 HIS   0.007   0.001   HIS H  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00599 (12841)
  covalent geometry    : angle       0.64234 (18575)
  hydrogen bonds       : bond        0.05124 (  750)
  hydrogen bonds       : angle       3.14015 ( 1879)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 90
  time to evaluate  : 0.302 
Fit side-chains
REVERT: B   35 ARG cc_start: 0.8084 (mtp180) cc_final: 0.7739 (mtm110)
REVERT: D   76 GLU cc_start: 0.8425 (tp30) cc_final: 0.8205 (tp30)
REVERT: E   65 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7797 (tt)
REVERT: E  120 MET cc_start: 0.8669 (mtt) cc_final: 0.8238 (mtt)
REVERT: F   95 ARG cc_start: 0.8039 (mtt-85) cc_final: 0.7714 (mtt-85)
REVERT: H   40 TYR cc_start: 0.8221 (t80) cc_final: 0.7838 (t80)
REVERT: G   72 ASP cc_start: 0.8080 (m-30) cc_final: 0.7585 (m-30)
REVERT: G   74 LYS cc_start: 0.8705 (mmtt) cc_final: 0.8286 (mppt)
  outliers start: 25
  outliers final: 6
  residues processed: 103
  average time/residue: 0.6838
  time to fit residues: 75.1640
Evaluate side-chains
  91 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain H residue   50 THR
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain G residue   19 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 93 optimal weight:    7.9990
   chunk 95 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9980
   chunk 62 optimal weight:    8.9990
   chunk 27 optimal weight:    5.9990
   chunk 54 optimal weight:   10.0000
   chunk 40 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 52 optimal weight:   20.0000
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  25 ASN
D  67 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.195655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.132943 restraints weight = 25073.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3592 rms_B_bonded: 2.23
r_work: 0.3342 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3333
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3333 r_free = 0.3333    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3333 r_free = 0.3333    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3333
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.1251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12841  Z= 0.160
  Angle     :  0.550   5.820  18575  Z= 0.332
  Chirality :  0.034   0.136   2108
  Planarity :  0.004   0.056   1346
  Dihedral  : 30.979 174.350   4001
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 21.79 %
    Favored  : 74.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.30), residues: 752
  helix:  1.64 (0.23), residues: 545
  sheet:  None (None), residues: 0
  loop : -1.26 (0.37), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 116 
 TYR   0.009   0.001   TYR F  72 
 PHE   0.011   0.002   PHE B  61 
 HIS   0.004   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (12841)
  covalent geometry    : angle       0.55033 (18575)
  hydrogen bonds       : bond        0.03773 (  750)
  hydrogen bonds       : angle       2.81478 ( 1879)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6714 (pm20)
REVERT: B   35 ARG cc_start: 0.8113 (mtp180) cc_final: 0.7876 (mtm110)
REVERT: D   76 GLU cc_start: 0.8496 (tp30) cc_final: 0.8295 (tp30)
REVERT: E  105 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7656 (mt-10)
REVERT: E  120 MET cc_start: 0.8548 (mtt) cc_final: 0.8311 (mtt)
REVERT: C   62 ILE cc_start: 0.8189 (mt) cc_final: 0.7974 (tt)
REVERT: G   72 ASP cc_start: 0.8031 (m-30) cc_final: 0.7628 (m-30)
  outliers start: 24
  outliers final: 12
  residues processed: 96
  average time/residue: 0.7140
  time to fit residues: 73.0354
Evaluate side-chains
  91 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain D residue   35 GLU
Chi-restraints excluded: chain D residue   49 HIS
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue  105 GLU
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   50 THR
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain C residue  107 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 7 optimal weight:    7.9990
   chunk 91 optimal weight:    0.6980
   chunk 73 optimal weight:   10.0000
   chunk 69 optimal weight:   10.0000
   chunk 38 optimal weight:    6.9990
   chunk 97 optimal weight:    0.6980
   chunk 80 optimal weight:    7.9990
   overall best weight:    2.4786

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
B  93 GLN
D  84 ASN
E 108 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.193834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.129264 restraints weight = 21217.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 2.04
r_work: 0.3330 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3319
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3319 r_free = 0.3319    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3319 r_free = 0.3319    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3319
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.1636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  12841  Z= 0.193
  Angle     :  0.571   5.714  18575  Z= 0.340
  Chirality :  0.035   0.129   2108
  Planarity :  0.005   0.054   1346
  Dihedral  : 31.169 172.435   4001
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 21.79 %
    Favored  : 73.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.30), residues: 752
  helix:  1.68 (0.23), residues: 545
  sheet:  None (None), residues: 0
  loop : -1.25 (0.37), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  72 
 TYR   0.011   0.001   TYR B  51 
 PHE   0.012   0.002   PHE B  61 
 HIS   0.004   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 (12841)
  covalent geometry    : angle       0.57143 (18575)
  hydrogen bonds       : bond        0.04183 (  750)
  hydrogen bonds       : angle       2.86771 ( 1879)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 82
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6812 (pm20)
REVERT: B   35 ARG cc_start: 0.8104 (mtp180) cc_final: 0.7871 (mtm110)
REVERT: D   76 GLU cc_start: 0.8491 (tp30) cc_final: 0.8236 (tp30)
REVERT: E  105 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7639 (mt-10)
REVERT: E  129 ARG cc_start: 0.7876 (tmt170) cc_final: 0.7641 (tmt170)
REVERT: C   92 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7933 (mt-10)
REVERT: G   72 ASP cc_start: 0.8029 (m-30) cc_final: 0.7652 (m-30)
  outliers start: 29
  outliers final: 13
  residues processed: 95
  average time/residue: 0.7000
  time to fit residues: 71.0948
Evaluate side-chains
  94 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 HIS
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain D residue   35 GLU
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue  105 GLU
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   50 THR
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain C residue   51 MET
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain G residue   19 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 52 optimal weight:   20.0000
   chunk 22 optimal weight:    5.9990
   chunk 74 optimal weight:   10.0000
   chunk 36 optimal weight:    0.8980
   chunk 38 optimal weight:    6.9990
   chunk 1 optimal weight:    4.9990
   chunk 78 optimal weight:   10.0000
   chunk 62 optimal weight:    8.9990
   chunk 88 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    3.3586

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
E  76 GLN
E 108 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.190580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.123900 restraints weight = 23762.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 2.16
r_work: 0.3279 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3284
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3284
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068  12841  Z= 0.230
  Angle     :  0.602   5.769  18575  Z= 0.354
  Chirality :  0.037   0.138   2108
  Planarity :  0.005   0.055   1346
  Dihedral  : 31.356 171.913   4001
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 21.00 %
    Favored  : 73.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.30), residues: 752
  helix:  1.57 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -1.31 (0.37), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  72 
 TYR   0.013   0.002   TYR A  54 
 PHE   0.013   0.002   PHE E  67 
 HIS   0.005   0.001   HIS H  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 (12841)
  covalent geometry    : angle       0.60191 (18575)
  hydrogen bonds       : bond        0.04531 (  750)
  hydrogen bonds       : angle       2.92413 ( 1879)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 83
  time to evaluate  : 0.192 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6821 (pm20)
REVERT: B   35 ARG cc_start: 0.8126 (mtp180) cc_final: 0.7890 (mtm110)
REVERT: B   93 GLN cc_start: 0.8255 (mt0) cc_final: 0.8013 (mt0)
REVERT: D   76 GLU cc_start: 0.8470 (tp30) cc_final: 0.8213 (tp30)
REVERT: D   90 THR cc_start: 0.8019 (OUTLIER) cc_final: 0.7788 (p)
REVERT: E   76 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8506 (tp-100)
REVERT: E  105 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7590 (mt-10)
REVERT: E  120 MET cc_start: 0.8613 (mtt) cc_final: 0.7755 (mtm)
REVERT: H  114 LYS cc_start: 0.8306 (tppp) cc_final: 0.7677 (ttmm)
REVERT: C   92 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7912 (mt-10)
REVERT: G   72 ASP cc_start: 0.8051 (m-30) cc_final: 0.7684 (m-30)
  outliers start: 34
  outliers final: 17
  residues processed: 98
  average time/residue: 0.6326
  time to fit residues: 66.1911
Evaluate side-chains
  103 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 81
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain D residue   35 GLU
Chi-restraints excluded: chain D residue   47 GLN
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue  105 GLU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   50 THR
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain C residue   51 MET
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain C residue   99 LYS
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   59 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 91 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 70 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 54 optimal weight:   10.0000
   chunk 22 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 53 optimal weight:   10.0000
   overall best weight:    1.1584

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.196629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.133185 restraints weight = 33150.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 2.38
r_work: 0.3336 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3326
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3326 r_free = 0.3326    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3326 r_free = 0.3326    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3326
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  12841  Z= 0.146
  Angle     :  0.538   5.690  18575  Z= 0.325
  Chirality :  0.034   0.136   2108
  Planarity :  0.004   0.052   1346
  Dihedral  : 31.048 173.740   4001
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 23.35 %
    Favored  : 73.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.83 (0.31), residues: 752
  helix:  2.03 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -1.05 (0.39), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  72 
 TYR   0.010   0.001   TYR F  72 
 PHE   0.015   0.002   PHE E  67 
 HIS   0.004   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (12841)
  covalent geometry    : angle       0.53757 (18575)
  hydrogen bonds       : bond        0.03463 (  750)
  hydrogen bonds       : angle       2.69373 ( 1879)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 0.289 
Fit side-chains
REVERT: B   35 ARG cc_start: 0.8122 (mtp180) cc_final: 0.7903 (mtm110)
REVERT: D   90 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.7849 (p)
REVERT: E  105 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7618 (mt-10)
REVERT: E  120 MET cc_start: 0.8516 (mtt) cc_final: 0.7714 (mtm)
REVERT: H  114 LYS cc_start: 0.8184 (tppp) cc_final: 0.7705 (ttmm)
REVERT: C   92 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7982 (mt-10)
REVERT: G   72 ASP cc_start: 0.8162 (m-30) cc_final: 0.7813 (m-30)
  outliers start: 21
  outliers final: 8
  residues processed: 96
  average time/residue: 0.7089
  time to fit residues: 72.4097
Evaluate side-chains
  91 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 HIS
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain D residue   35 GLU
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue  105 GLU
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   50 THR
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain G residue  114 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 95 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   chunk 4 optimal weight:    0.0870
   chunk 21 optimal weight:    4.9990
   chunk 32 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   chunk 63 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 89 optimal weight:    9.9990
   overall best weight:    1.1160

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.196897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.132387 restraints weight = 21390.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 1.99
r_work: 0.3385 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3394
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3394 r_free = 0.3394    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3394 r_free = 0.3394    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3394
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.2173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  12841  Z= 0.145
  Angle     :  0.531   5.652  18575  Z= 0.320
  Chirality :  0.033   0.134   2108
  Planarity :  0.004   0.052   1346
  Dihedral  : 31.025 172.389   4001
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 23.20 %
    Favored  : 73.82 %
  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:  2.07 (0.31), residues: 752
  helix:  2.19 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -0.92 (0.39), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  53 
 TYR   0.009   0.001   TYR G  57 
 PHE   0.016   0.002   PHE D  65 
 HIS   0.004   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (12841)
  covalent geometry    : angle       0.53113 (18575)
  hydrogen bonds       : bond        0.03460 (  750)
  hydrogen bonds       : angle       2.65397 ( 1879)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.337 
Fit side-chains
REVERT: D   90 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7813 (p)
REVERT: E  105 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7563 (mt-10)
REVERT: H  114 LYS cc_start: 0.8179 (tppp) cc_final: 0.7710 (ttmm)
REVERT: G   72 ASP cc_start: 0.8181 (m-30) cc_final: 0.7820 (m-30)
REVERT: G   74 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8284 (mppt)
  outliers start: 19
  outliers final: 10
  residues processed: 92
  average time/residue: 0.6857
  time to fit residues: 67.0573
Evaluate side-chains
  95 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain D residue   35 GLU
Chi-restraints excluded: chain D residue   47 GLN
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue  105 GLU
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   50 THR
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue  114 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 57 optimal weight:   10.0000
   chunk 12 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9980
   chunk 96 optimal weight:    9.9990
   chunk 1 optimal weight:    4.9990
   chunk 69 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 38 optimal weight:    4.9990
   chunk 66 optimal weight:   20.0000
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
D  84 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.191396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.123304 restraints weight = 31130.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 2.43
r_work: 0.3261 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3271
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3271 r_free = 0.3271    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3271 r_free = 0.3271    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3271
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  12841  Z= 0.234
  Angle     :  0.599   5.757  18575  Z= 0.352
  Chirality :  0.037   0.137   2108
  Planarity :  0.005   0.053   1346
  Dihedral  : 31.306 170.709   4001
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 22.57 %
    Favored  : 73.04 %
  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:  1.56 (0.30), residues: 752
  helix:  1.80 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.04 (0.39), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  53 
 TYR   0.018   0.002   TYR A  54 
 PHE   0.014   0.002   PHE D  65 
 HIS   0.004   0.001   HIS H  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00546 (12841)
  covalent geometry    : angle       0.59939 (18575)
  hydrogen bonds       : bond        0.04496 (  750)
  hydrogen bonds       : angle       2.91594 ( 1879)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 86
  time to evaluate  : 0.191 
Fit side-chains
REVERT: D   90 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7857 (p)
REVERT: E  105 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7645 (mt-10)
REVERT: G   72 ASP cc_start: 0.8189 (m-30) cc_final: 0.7790 (m-30)
REVERT: G   74 LYS cc_start: 0.8755 (mmtt) cc_final: 0.8327 (mppt)
  outliers start: 28
  outliers final: 17
  residues processed: 102
  average time/residue: 0.6351
  time to fit residues: 69.4653
Evaluate side-chains
  101 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain D residue   35 GLU
Chi-restraints excluded: chain D residue   47 GLN
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue  105 GLU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   50 THR
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain C residue   51 MET
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue  114 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 89 optimal weight:    0.6980
   chunk 56 optimal weight:   10.0000
   chunk 16 optimal weight:    0.1980
   chunk 48 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 78 optimal weight:   10.0000
   chunk 60 optimal weight:    8.9990
   chunk 30 optimal weight:    4.9990
   chunk 63 optimal weight:   10.0000
   overall best weight:    0.6380

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.197380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.130710 restraints weight = 26683.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 2.26
r_work: 0.3359 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3365
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3365 r_free = 0.3365    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3365 r_free = 0.3365    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3365
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12841  Z= 0.138
  Angle     :  0.533   7.416  18575  Z= 0.321
  Chirality :  0.033   0.138   2108
  Planarity :  0.004   0.052   1346
  Dihedral  : 30.922 172.983   4001
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 24.76 %
    Favored  : 73.04 %
  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:  2.14 (0.31), residues: 752
  helix:  2.24 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -0.89 (0.39), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  35 
 TYR   0.010   0.001   TYR F  72 
 PHE   0.019   0.002   PHE D  65 
 HIS   0.004   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (12841)
  covalent geometry    : angle       0.53322 (18575)
  hydrogen bonds       : bond        0.03325 (  750)
  hydrogen bonds       : angle       2.64897 ( 1879)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.345 
Fit side-chains
REVERT: B   27 GLN cc_start: 0.8698 (mt0) cc_final: 0.8447 (mp10)
REVERT: D   51 ASP cc_start: 0.8696 (m-30) cc_final: 0.8435 (t0)
REVERT: D   90 THR cc_start: 0.8108 (OUTLIER) cc_final: 0.7876 (p)
REVERT: E   42 ARG cc_start: 0.7653 (mmt90) cc_final: 0.6292 (mmm-85)
REVERT: H  114 LYS cc_start: 0.8409 (tppp) cc_final: 0.7876 (ttmm)
REVERT: G   59 THR cc_start: 0.9068 (m) cc_final: 0.8669 (m)
REVERT: G   72 ASP cc_start: 0.8185 (m-30) cc_final: 0.7841 (m-30)
REVERT: G   74 LYS cc_start: 0.8734 (mmtt) cc_final: 0.8296 (mppt)
  outliers start: 14
  outliers final: 10
  residues processed: 97
  average time/residue: 0.7483
  time to fit residues: 77.0588
Evaluate side-chains
  96 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain D residue   35 GLU
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   50 THR
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain G residue  114 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 83 optimal weight:    0.5980
   chunk 40 optimal weight:    0.6980
   chunk 68 optimal weight:   10.0000
   chunk 25 optimal weight:    5.9990
   chunk 86 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
D  67 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.196961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.129098 restraints weight = 28427.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 2.33
r_work: 0.3340 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3351
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3351 r_free = 0.3351    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3351 r_free = 0.3351    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3351
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.2515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  12841  Z= 0.149
  Angle     :  0.539   7.366  18575  Z= 0.322
  Chirality :  0.033   0.132   2108
  Planarity :  0.004   0.054   1346
  Dihedral  : 30.931 172.165   4001
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 25.71 %
    Favored  : 72.26 %
  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:  2.16 (0.30), residues: 752
  helix:  2.26 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -0.86 (0.40), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG B  35 
 TYR   0.014   0.001   TYR A  54 
 PHE   0.017   0.002   PHE D  65 
 HIS   0.004   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (12841)
  covalent geometry    : angle       0.53867 (18575)
  hydrogen bonds       : bond        0.03486 (  750)
  hydrogen bonds       : angle       2.67329 ( 1879)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.309 
Fit side-chains
REVERT: B   27 GLN cc_start: 0.8706 (mt0) cc_final: 0.8468 (mp10)
REVERT: B   35 ARG cc_start: 0.7749 (mtm110) cc_final: 0.7539 (mtp180)
REVERT: D   35 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7928 (pm20)
REVERT: D   51 ASP cc_start: 0.8661 (m-30) cc_final: 0.8398 (t0)
REVERT: D   90 THR cc_start: 0.8125 (OUTLIER) cc_final: 0.7874 (p)
REVERT: E   42 ARG cc_start: 0.7668 (mmt90) cc_final: 0.6282 (mmm-85)
REVERT: H  114 LYS cc_start: 0.8403 (tppp) cc_final: 0.7840 (ttmm)
REVERT: G   72 ASP cc_start: 0.8234 (m-30) cc_final: 0.7931 (m-30)
REVERT: G   74 LYS cc_start: 0.8785 (mmtt) cc_final: 0.8367 (mppt)
  outliers start: 13
  outliers final: 9
  residues processed: 92
  average time/residue: 0.7125
  time to fit residues: 69.5984
Evaluate side-chains
  96 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain D residue   35 GLU
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   50 THR
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue  114 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 28 optimal weight:    3.9990
   chunk 63 optimal weight:   10.0000
   chunk 56 optimal weight:   10.0000
   chunk 66 optimal weight:   20.0000
   chunk 30 optimal weight:    8.9990
   chunk 7 optimal weight:    7.9990
   chunk 76 optimal weight:   10.0000
   chunk 10 optimal weight:    1.9990
   chunk 87 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    4.1990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.190676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.122920 restraints weight = 28304.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 2.34
r_work: 0.3255 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3267
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3267 r_free = 0.3267    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3267 r_free = 0.3267    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3267
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.2501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069  12841  Z= 0.270
  Angle     :  0.639   7.585  18575  Z= 0.369
  Chirality :  0.039   0.142   2108
  Planarity :  0.005   0.057   1346
  Dihedral  : 31.348 169.710   4001
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 25.08 %
    Favored  : 71.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.41 (0.30), residues: 752
  helix:  1.69 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.11 (0.39), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B  35 
 TYR   0.025   0.002   TYR A  54 
 PHE   0.015   0.002   PHE D  65 
 HIS   0.004   0.001   HIS H  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00636 (12841)
  covalent geometry    : angle       0.63863 (18575)
  hydrogen bonds       : bond        0.04889 (  750)
  hydrogen bonds       : angle       3.01242 ( 1879)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3558.03 seconds
wall clock time: 61 minutes 10.79 seconds (3670.79 seconds total)