Starting phenix.real_space_refine
on Thu May 15 05:29:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ip3_35630/05_2025/8ip3_35630.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ip3_35630/05_2025/8ip3_35630.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ip3_35630/05_2025/8ip3_35630.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ip3_35630/05_2025/8ip3_35630.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ip3_35630/05_2025/8ip3_35630.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ip3_35630/05_2025/8ip3_35630.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.027
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: 6
    Type Number    sf(0)   Gaussians
     Mg     12      5.21       5
     S      65      5.16       5
     Cl      1      4.86       5
     C    8275      2.51       5
     N    2155      2.21       5
     O    2360      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 12868
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2571
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 319, 2571
          Classifications: {'peptide': 319}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 8, 'TRANS': 310}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' CL': 1, ' MG': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' MG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "E"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 5.54, per 1000 atoms: 0.43
  Number of scatterers: 12868
  At special positions: 0
  Unit cell: (108.81, 106.95, 141.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      1     17.00
     S      65     16.00
     Mg     12     11.99
     O    2360      8.00
     N    2155      7.00
     C    8275      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.83
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3040

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 5 sheets defined
      72.4% alpha, 9.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 104 through 112
    Processing helix  chain 'A' and resid 114 through 119
      removed outlier: 3.564A  pdb=" N   ARG A 119 " --> pdb=" O   ARG A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 173
      Proline residue:  A 168  - end of helix
    Processing helix  chain 'A' and resid 183 through 219
      removed outlier: 3.625A  pdb=" N   ARG A 187 " --> pdb=" O   PRO A 183 " (cutoff:3.500A)
      Proline residue:  A 209  - end of helix
    Processing helix  chain 'A' and resid 227 through 261
      removed outlier: 4.050A  pdb=" N   GLU A 261 " --> pdb=" O   GLU A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 269
      removed outlier: 3.516A  pdb=" N   LEU A 265 " --> pdb=" O   GLU A 261 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   CYS A 269 " --> pdb=" O   LEU A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 275
      removed outlier: 3.932A  pdb=" N   ASP A 275 " --> pdb=" O   SER A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 283
      removed outlier: 4.099A  pdb=" N   LYS A 281 " --> pdb=" O   GLN A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 359
    Processing helix  chain 'A' and resid 371 through 401
      removed outlier: 4.425A  pdb=" N   TRP A 375 " --> pdb=" O   HIS A 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 112
    Processing helix  chain 'B' and resid 114 through 119
      removed outlier: 3.565A  pdb=" N   ARG B 119 " --> pdb=" O   ARG B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 173
      Proline residue:  B 168  - end of helix
    Processing helix  chain 'B' and resid 183 through 219
      removed outlier: 3.625A  pdb=" N   ARG B 187 " --> pdb=" O   PRO B 183 " (cutoff:3.500A)
      Proline residue:  B 209  - end of helix
    Processing helix  chain 'B' and resid 227 through 261
      removed outlier: 4.051A  pdb=" N   GLU B 261 " --> pdb=" O   GLU B 257 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 261 through 269
      removed outlier: 3.517A  pdb=" N   LEU B 265 " --> pdb=" O   GLU B 261 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   CYS B 269 " --> pdb=" O   LEU B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 275
      removed outlier: 3.932A  pdb=" N   ASP B 275 " --> pdb=" O   SER B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 283
      removed outlier: 4.099A  pdb=" N   LYS B 281 " --> pdb=" O   GLN B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 359
    Processing helix  chain 'B' and resid 371 through 401
      removed outlier: 4.424A  pdb=" N   TRP B 375 " --> pdb=" O   HIS B 371 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 104 through 112
    Processing helix  chain 'C' and resid 114 through 119
      removed outlier: 3.564A  pdb=" N   ARG C 119 " --> pdb=" O   ARG C 116 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 173
      Proline residue:  C 168  - end of helix
    Processing helix  chain 'C' and resid 183 through 219
      removed outlier: 3.625A  pdb=" N   ARG C 187 " --> pdb=" O   PRO C 183 " (cutoff:3.500A)
      Proline residue:  C 209  - end of helix
    Processing helix  chain 'C' and resid 227 through 261
      removed outlier: 4.051A  pdb=" N   GLU C 261 " --> pdb=" O   GLU C 257 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 261 through 269
      removed outlier: 3.516A  pdb=" N   LEU C 265 " --> pdb=" O   GLU C 261 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   CYS C 269 " --> pdb=" O   LEU C 265 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 269 through 275
      removed outlier: 3.931A  pdb=" N   ASP C 275 " --> pdb=" O   SER C 271 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 275 through 283
      removed outlier: 4.099A  pdb=" N   LYS C 281 " --> pdb=" O   GLN C 277 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 287 through 359
    Processing helix  chain 'C' and resid 371 through 401
      removed outlier: 4.425A  pdb=" N   TRP C 375 " --> pdb=" O   HIS C 371 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 112
    Processing helix  chain 'D' and resid 114 through 119
      removed outlier: 3.565A  pdb=" N   ARG D 119 " --> pdb=" O   ARG D 116 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 159 through 173
      Proline residue:  D 168  - end of helix
    Processing helix  chain 'D' and resid 183 through 219
      removed outlier: 3.625A  pdb=" N   ARG D 187 " --> pdb=" O   PRO D 183 " (cutoff:3.500A)
      Proline residue:  D 209  - end of helix
    Processing helix  chain 'D' and resid 227 through 261
      removed outlier: 4.050A  pdb=" N   GLU D 261 " --> pdb=" O   GLU D 257 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 261 through 269
      removed outlier: 3.517A  pdb=" N   LEU D 265 " --> pdb=" O   GLU D 261 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   CYS D 269 " --> pdb=" O   LEU D 265 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 269 through 275
      removed outlier: 3.932A  pdb=" N   ASP D 275 " --> pdb=" O   SER D 271 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 275 through 283
      removed outlier: 4.099A  pdb=" N   LYS D 281 " --> pdb=" O   GLN D 277 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 287 through 359
    Processing helix  chain 'D' and resid 371 through 401
      removed outlier: 4.425A  pdb=" N   TRP D 375 " --> pdb=" O   HIS D 371 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 104 through 112
    Processing helix  chain 'E' and resid 114 through 119
      removed outlier: 3.565A  pdb=" N   ARG E 119 " --> pdb=" O   ARG E 116 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 159 through 173
      Proline residue:  E 168  - end of helix
    Processing helix  chain 'E' and resid 183 through 219
      removed outlier: 3.625A  pdb=" N   ARG E 187 " --> pdb=" O   PRO E 183 " (cutoff:3.500A)
      Proline residue:  E 209  - end of helix
    Processing helix  chain 'E' and resid 227 through 261
      removed outlier: 4.051A  pdb=" N   GLU E 261 " --> pdb=" O   GLU E 257 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 261 through 269
      removed outlier: 3.517A  pdb=" N   LEU E 265 " --> pdb=" O   GLU E 261 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   CYS E 269 " --> pdb=" O   LEU E 265 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 269 through 275
      removed outlier: 3.932A  pdb=" N   ASP E 275 " --> pdb=" O   SER E 271 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 275 through 283
      removed outlier: 4.099A  pdb=" N   LYS E 281 " --> pdb=" O   GLN E 277 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 287 through 359
    Processing helix  chain 'E' and resid 371 through 401
      removed outlier: 4.424A  pdb=" N   TRP E 375 " --> pdb=" O   HIS E 371 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 103
      removed outlier: 4.191A  pdb=" N   LYS A 141 " --> pdb=" O   LEU A 152 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 103
      removed outlier: 4.192A  pdb=" N   LYS B 141 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 97 through 103
      removed outlier: 4.192A  pdb=" N   LYS C 141 " --> pdb=" O   LEU C 152 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 97 through 103
      removed outlier: 4.192A  pdb=" N   LYS D 141 " --> pdb=" O   LEU D 152 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 97 through 103
      removed outlier: 4.192A  pdb=" N   LYS E 141 " --> pdb=" O   LEU E 152 " (cutoff:3.500A)

    1015 hydrogen bonds defined for protein.
    2970 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.02

  Time building geometry restraints manager: 3.35 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4210
        1.34 -     1.46: 2437
        1.46 -     1.58: 6318
        1.58 -     1.69: 0
        1.69 -     1.81: 120
  Bond restraints: 13085
  Sorted by residual:
  bond pdb=" C   SER B 348 "
       pdb=" O   SER B 348 "
    ideal  model  delta    sigma   weight residual
    1.237  1.245 -0.008 1.17e-02 7.31e+03 5.01e-01
  bond pdb=" C   SER E 348 "
       pdb=" O   SER E 348 "
    ideal  model  delta    sigma   weight residual
    1.237  1.245 -0.008 1.17e-02 7.31e+03 4.74e-01
  bond pdb=" CA  LEU D 354 "
       pdb=" C   LEU D 354 "
    ideal  model  delta    sigma   weight residual
    1.523  1.515  0.008 1.30e-02 5.92e+03 4.19e-01
  bond pdb=" CA  LEU C 354 "
       pdb=" C   LEU C 354 "
    ideal  model  delta    sigma   weight residual
    1.523  1.515  0.008 1.30e-02 5.92e+03 4.11e-01
  bond pdb=" C   SER D 348 "
       pdb=" O   SER D 348 "
    ideal  model  delta    sigma   weight residual
    1.237  1.244 -0.007 1.17e-02 7.31e+03 4.03e-01
  ... (remaining 13080 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.04: 17215
        1.04 -     2.09: 375
        2.09 -     3.13: 55
        3.13 -     4.17: 20
        4.17 -     5.21: 20
  Bond angle restraints: 17685
  Sorted by residual:
  angle pdb=" C   LEU E 351 "
        pdb=" N   PHE E 352 "
        pdb=" CA  PHE E 352 "
      ideal   model   delta    sigma   weight residual
     121.14  117.47    3.67 1.75e+00 3.27e-01 4.41e+00
  angle pdb=" C   LEU C 351 "
        pdb=" N   PHE C 352 "
        pdb=" CA  PHE C 352 "
      ideal   model   delta    sigma   weight residual
     121.14  117.47    3.67 1.75e+00 3.27e-01 4.39e+00
  angle pdb=" C   LEU B 351 "
        pdb=" N   PHE B 352 "
        pdb=" CA  PHE B 352 "
      ideal   model   delta    sigma   weight residual
     121.14  117.47    3.67 1.75e+00 3.27e-01 4.39e+00
  angle pdb=" C   LEU A 351 "
        pdb=" N   PHE A 352 "
        pdb=" CA  PHE A 352 "
      ideal   model   delta    sigma   weight residual
     121.14  117.47    3.67 1.75e+00 3.27e-01 4.39e+00
  angle pdb=" C   LEU D 351 "
        pdb=" N   PHE D 352 "
        pdb=" CA  PHE D 352 "
      ideal   model   delta    sigma   weight residual
     121.14  117.48    3.66 1.75e+00 3.27e-01 4.37e+00
  ... (remaining 17680 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.51: 7428
       17.51 -    35.03: 462
       35.03 -    52.54: 35
       52.54 -    70.05: 5
       70.05 -    87.57: 5
  Dihedral angle restraints: 7935
    sinusoidal: 3270
      harmonic: 4665
  Sorted by residual:
  dihedral pdb=" CB  GLU E 147 "
           pdb=" CG  GLU E 147 "
           pdb=" CD  GLU E 147 "
           pdb=" OE1 GLU E 147 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.57  -87.57     1      3.00e+01 1.11e-03 1.02e+01
  dihedral pdb=" CB  GLU D 147 "
           pdb=" CG  GLU D 147 "
           pdb=" CD  GLU D 147 "
           pdb=" OE1 GLU D 147 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.54  -87.54     1      3.00e+01 1.11e-03 1.02e+01
  dihedral pdb=" CB  GLU B 147 "
           pdb=" CG  GLU B 147 "
           pdb=" CD  GLU B 147 "
           pdb=" OE1 GLU B 147 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.54  -87.54     1      3.00e+01 1.11e-03 1.02e+01
  ... (remaining 7932 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1379
       0.029 -    0.058: 420
       0.058 -    0.086: 156
       0.086 -    0.115: 75
       0.115 -    0.144: 20
  Chirality restraints: 2050
  Sorted by residual:
  chirality pdb=" CA  LEU A 167 "
            pdb=" N   LEU A 167 "
            pdb=" C   LEU A 167 "
            pdb=" CB  LEU A 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.16e-01
  chirality pdb=" CA  LEU C 167 "
            pdb=" N   LEU C 167 "
            pdb=" C   LEU C 167 "
            pdb=" CB  LEU C 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.16e-01
  chirality pdb=" CA  LEU B 167 "
            pdb=" N   LEU B 167 "
            pdb=" C   LEU B 167 "
            pdb=" CB  LEU B 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.09e-01
  ... (remaining 2047 not shown)

  Planarity restraints: 2235
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 163 "    0.011 2.00e-02 2.50e+03   2.17e-02 4.71e+00
        pdb=" C   LEU B 163 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   LEU B 163 "    0.014 2.00e-02 2.50e+03
        pdb=" N   PHE B 164 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU E 163 "   -0.011 2.00e-02 2.50e+03   2.16e-02 4.66e+00
        pdb=" C   LEU E 163 "    0.037 2.00e-02 2.50e+03
        pdb=" O   LEU E 163 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   PHE E 164 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 163 "    0.011 2.00e-02 2.50e+03   2.14e-02 4.58e+00
        pdb=" C   LEU A 163 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   LEU A 163 "    0.014 2.00e-02 2.50e+03
        pdb=" N   PHE A 164 "    0.012 2.00e-02 2.50e+03
  ... (remaining 2232 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2582
        2.78 -     3.31: 13000
        3.31 -     3.84: 21592
        3.84 -     4.37: 25684
        4.37 -     4.90: 45039
  Nonbonded interactions: 107897
  Sorted by model distance:
  nonbonded pdb=" OG  SER D  99 "
            pdb=" OH  TYR D 154 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OG  SER E  99 "
            pdb=" OH  TYR E 154 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OG  SER C  99 "
            pdb=" OH  TYR C 154 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OG  SER B  99 "
            pdb=" OH  TYR B 154 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OG  SER A  99 "
            pdb=" OH  TYR A 154 "
     model   vdw
     2.256 3.040
  ... (remaining 107892 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' and (resid 83 through 401 or resid 502))
  selection = (chain 'B' and (resid 83 through 401 or resid 502))
  selection = (chain 'C' and (resid 83 through 401 or resid 502))
  selection = (chain 'D' and (resid 83 through 401 or resid 502))
  selection = (chain 'E' and (resid 83 through 401 or resid 502))
}

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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.050
  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:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     26.500
  Find NCS groups from input model:        0.650
  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:11.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
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      :  0.002   0.018  13085  Z= 0.116
  Angle     :  0.425   5.214  17685  Z= 0.224
  Chirality :  0.037   0.144   2050
  Planarity :  0.003   0.029   2235
  Dihedral  : 10.758  87.566   4895
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.79 (0.21), residues: 1585
  helix:  3.32 (0.15), residues: 1040
  sheet:  2.16 (0.38), residues: 145
  loop :  0.33 (0.34), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 162 
 HIS   0.001   0.000   HIS C 223 
 PHE   0.016   0.001   PHE D 352 
 TYR   0.012   0.001   TYR E 299 
 ARG   0.001   0.000   ARG B 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08434 ( 1015)
  hydrogen bonds       : angle       4.40704 ( 2970)
  covalent geometry    : bond        0.00236 (13085)
  covalent geometry    : angle       0.42491 (17685)

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

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

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 1.501 
Fit side-chains
REVERT: A  383 MET cc_start: 0.6980 (mmp) cc_final: 0.6550 (mtp)
REVERT: C  383 MET cc_start: 0.6789 (mmp) cc_final: 0.6236 (mtm)
REVERT: D  383 MET cc_start: 0.6884 (mmp) cc_final: 0.6458 (mtp)
REVERT: E  383 MET cc_start: 0.7061 (mmp) cc_final: 0.6482 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 208
  average time/residue: 1.2699
  time to fit residues: 287.2921
Evaluate side-chains
  152 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 1.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 130 optimal weight:    1.9990
   chunk 117 optimal weight:    3.9990
   chunk 65 optimal weight:    0.0870
   chunk 40 optimal weight:   10.0000
   chunk 79 optimal weight:    4.9990
   chunk 62 optimal weight:    6.9990
   chunk 121 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 90 optimal weight:    7.9990
   chunk 140 optimal weight:    2.9990
   overall best weight:    2.2166

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

Flipped N/Q/H residues before XYZ refinement:
A 121 GLN
B 121 GLN
E 362 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.109177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.080854 restraints weight = 20131.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 2.56
r_work: 0.2827 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.1222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  13085  Z= 0.235
  Angle     :  0.536   8.016  17685  Z= 0.278
  Chirality :  0.042   0.216   2050
  Planarity :  0.004   0.032   2235
  Dihedral  :  4.003  14.119   1720
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  6.71 %
    Favored  : 92.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.50 (0.21), residues: 1585
  helix:  3.16 (0.15), residues: 1020
  sheet:  2.05 (0.39), residues: 145
  loop :  0.19 (0.35), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 196 
 HIS   0.003   0.001   HIS C 122 
 PHE   0.023   0.002   PHE A 395 
 TYR   0.025   0.002   TYR C 299 
 ARG   0.004   0.000   ARG B 165 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05250 ( 1015)
  hydrogen bonds       : angle       4.12468 ( 2970)
  covalent geometry    : bond        0.00547 (13085)
  covalent geometry    : angle       0.53572 (17685)

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

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

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 156
  time to evaluate  : 1.576 
Fit side-chains
REVERT: A   94 GLN cc_start: 0.8259 (mp10) cc_final: 0.7860 (mp10)
REVERT: A  383 MET cc_start: 0.7059 (mmp) cc_final: 0.6409 (mtp)
REVERT: C  350 SER cc_start: 0.8155 (t) cc_final: 0.7913 (m)
REVERT: C  383 MET cc_start: 0.6989 (mmp) cc_final: 0.6305 (mtm)
REVERT: D  350 SER cc_start: 0.8489 (OUTLIER) cc_final: 0.8251 (p)
REVERT: D  383 MET cc_start: 0.6961 (mmp) cc_final: 0.6296 (mtp)
REVERT: E   94 GLN cc_start: 0.8243 (mp10) cc_final: 0.7728 (mp10)
REVERT: E  350 SER cc_start: 0.8282 (t) cc_final: 0.7882 (p)
REVERT: E  355 MET cc_start: 0.8090 (ttm) cc_final: 0.7818 (ttm)
REVERT: E  362 ASN cc_start: 0.7898 (m110) cc_final: 0.7643 (m-40)
REVERT: E  383 MET cc_start: 0.7116 (mmp) cc_final: 0.6296 (mtp)
  outliers start: 14
  outliers final: 5
  residues processed: 160
  average time/residue: 1.1620
  time to fit residues: 203.6154
Evaluate side-chains
  145 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 139
  time to evaluate  : 1.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  350 SER
Chi-restraints excluded: chain D residue  355 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 152 optimal weight:    9.9990
   chunk 135 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 129 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 105 optimal weight:    0.8980
   chunk 56 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
B 121 GLN
B 362 ASN
E 121 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.109543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.080846 restraints weight = 19853.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3069 rms_B_bonded: 2.51
r_work: 0.2901 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.1370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  13085  Z= 0.191
  Angle     :  0.495   8.769  17685  Z= 0.260
  Chirality :  0.041   0.215   2050
  Planarity :  0.004   0.036   2235
  Dihedral  :  3.977  14.332   1720
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  7.28 %
    Favored  : 90.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.44 (0.21), residues: 1585
  helix:  2.87 (0.15), residues: 1050
  sheet:  2.06 (0.40), residues: 145
  loop :  0.69 (0.36), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 375 
 HIS   0.002   0.001   HIS C 122 
 PHE   0.019   0.002   PHE A 352 
 TYR   0.020   0.002   TYR C 299 
 ARG   0.003   0.000   ARG B 165 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05034 ( 1015)
  hydrogen bonds       : angle       4.03471 ( 2970)
  covalent geometry    : bond        0.00440 (13085)
  covalent geometry    : angle       0.49509 (17685)

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

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

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 161
  time to evaluate  : 1.682 
Fit side-chains
REVERT: A   94 GLN cc_start: 0.8194 (mp10) cc_final: 0.7787 (mp10)
REVERT: A  359 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7715 (t80)
REVERT: A  383 MET cc_start: 0.6772 (mmp) cc_final: 0.6156 (mtp)
REVERT: B  355 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7759 (ttp)
REVERT: B  359 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7772 (t80)
REVERT: B  362 ASN cc_start: 0.7871 (m110) cc_final: 0.7611 (m-40)
REVERT: B  383 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.6311 (mpp)
REVERT: C  383 MET cc_start: 0.6935 (mmp) cc_final: 0.6223 (mtm)
REVERT: D  359 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7659 (t80)
REVERT: D  383 MET cc_start: 0.6858 (mmp) cc_final: 0.6229 (mtp)
REVERT: D  391 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6545 (ttp-170)
REVERT: E   94 GLN cc_start: 0.8203 (mp10) cc_final: 0.7766 (mp10)
REVERT: E  350 SER cc_start: 0.8118 (t) cc_final: 0.7750 (p)
REVERT: E  355 MET cc_start: 0.8019 (ttm) cc_final: 0.7783 (ttm)
REVERT: E  383 MET cc_start: 0.6933 (mmp) cc_final: 0.6135 (mtp)
  outliers start: 25
  outliers final: 7
  residues processed: 169
  average time/residue: 1.1746
  time to fit residues: 217.7960
Evaluate side-chains
  163 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 150
  time to evaluate  : 1.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain B residue  257 GLU
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain B residue  359 PHE
Chi-restraints excluded: chain B residue  383 MET
Chi-restraints excluded: chain D residue  314 ARG
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  355 MET
Chi-restraints excluded: chain D residue  359 PHE
Chi-restraints excluded: chain D residue  391 ARG
Chi-restraints excluded: chain E residue  338 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 122 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 151 optimal weight:    4.9990
   chunk 84 optimal weight:    4.9990
   chunk 71 optimal weight:    9.9990
   chunk 109 optimal weight:    2.9990
   chunk 134 optimal weight:    0.7980
   chunk 63 optimal weight:    0.0870
   chunk 70 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.9360

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

Flipped N/Q/H residues before XYZ refinement:
C 362 ASN
D 121 GLN
E 121 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.111175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.082755 restraints weight = 19535.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 2.51
r_work: 0.2942 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.1337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  13085  Z= 0.131
  Angle     :  0.454   9.282  17685  Z= 0.239
  Chirality :  0.039   0.234   2050
  Planarity :  0.003   0.038   2235
  Dihedral  :  3.821  14.243   1720
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  :  9.05 %
    Favored  : 89.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.56 (0.21), residues: 1585
  helix:  2.98 (0.15), residues: 1050
  sheet:  2.10 (0.40), residues: 145
  loop :  0.69 (0.36), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 162 
 HIS   0.002   0.000   HIS C 122 
 PHE   0.019   0.001   PHE C 352 
 TYR   0.017   0.001   TYR C 299 
 ARG   0.003   0.000   ARG C 165 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04687 ( 1015)
  hydrogen bonds       : angle       3.90634 ( 2970)
  covalent geometry    : bond        0.00281 (13085)
  covalent geometry    : angle       0.45373 (17685)

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

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

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 160
  time to evaluate  : 1.390 
Fit side-chains
REVERT: A   94 GLN cc_start: 0.8187 (mp10) cc_final: 0.7724 (mp10)
REVERT: A  359 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.7571 (t80)
REVERT: A  383 MET cc_start: 0.6764 (mmp) cc_final: 0.6146 (mtp)
REVERT: C  383 MET cc_start: 0.6825 (mmp) cc_final: 0.6123 (mtm)
REVERT: D  359 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7765 (t80)
REVERT: D  383 MET cc_start: 0.6775 (mmp) cc_final: 0.6131 (mtp)
REVERT: D  391 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.6474 (ttp-170)
REVERT: E   94 GLN cc_start: 0.8206 (mp10) cc_final: 0.7659 (mp10)
REVERT: E  350 SER cc_start: 0.8120 (t) cc_final: 0.7736 (p)
REVERT: E  355 MET cc_start: 0.7954 (ttm) cc_final: 0.7694 (ttm)
REVERT: E  383 MET cc_start: 0.6831 (mmp) cc_final: 0.6010 (mtp)
  outliers start: 22
  outliers final: 8
  residues processed: 168
  average time/residue: 1.1781
  time to fit residues: 216.9814
Evaluate side-chains
  166 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 155
  time to evaluate  : 1.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain B residue  257 GLU
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain C residue  197 ILE
Chi-restraints excluded: chain C residue  359 PHE
Chi-restraints excluded: chain D residue  314 ARG
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  355 MET
Chi-restraints excluded: chain D residue  359 PHE
Chi-restraints excluded: chain D residue  391 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 107 optimal weight:    4.9990
   chunk 128 optimal weight:    5.9990
   chunk 145 optimal weight:    0.9980
   chunk 116 optimal weight:    3.9990
   chunk 125 optimal weight:    0.4980
   chunk 143 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0470
   chunk 95 optimal weight:    5.9990
   chunk 64 optimal weight:    5.9990
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.6278

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

Flipped N/Q/H residues before XYZ refinement:
D 121 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.112303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.084038 restraints weight = 19717.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 2.52
r_work: 0.2972 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.1337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  13085  Z= 0.113
  Angle     :  0.432   5.681  17685  Z= 0.230
  Chirality :  0.039   0.215   2050
  Planarity :  0.003   0.038   2235
  Dihedral  :  3.714  14.410   1720
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  9.05 %
    Favored  : 89.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.66 (0.21), residues: 1585
  helix:  3.04 (0.15), residues: 1065
  sheet:  2.07 (0.40), residues: 145
  loop :  0.71 (0.37), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 162 
 HIS   0.002   0.000   HIS C 122 
 PHE   0.021   0.001   PHE E 352 
 TYR   0.016   0.001   TYR C 299 
 ARG   0.004   0.000   ARG C 372 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04482 ( 1015)
  hydrogen bonds       : angle       3.80065 ( 2970)
  covalent geometry    : bond        0.00227 (13085)
  covalent geometry    : angle       0.43161 (17685)

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

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

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 163
  time to evaluate  : 1.482 
Fit side-chains
REVERT: A   94 GLN cc_start: 0.8190 (mp10) cc_final: 0.7726 (mp10)
REVERT: A  383 MET cc_start: 0.6831 (mmp) cc_final: 0.6152 (mtp)
REVERT: C  383 MET cc_start: 0.6690 (mmp) cc_final: 0.5963 (mtm)
REVERT: D  359 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7635 (t80)
REVERT: D  383 MET cc_start: 0.6737 (mmp) cc_final: 0.6090 (mtp)
REVERT: E   94 GLN cc_start: 0.8261 (mp10) cc_final: 0.7759 (mp10)
REVERT: E  314 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.6849 (mmp80)
REVERT: E  355 MET cc_start: 0.7855 (ttm) cc_final: 0.7538 (ttm)
REVERT: E  383 MET cc_start: 0.6763 (mmp) cc_final: 0.5969 (mtp)
  outliers start: 23
  outliers final: 8
  residues processed: 170
  average time/residue: 1.2099
  time to fit residues: 225.4537
Evaluate side-chains
  167 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 157
  time to evaluate  : 1.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  257 GLU
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain C residue  197 ILE
Chi-restraints excluded: chain D residue  257 GLU
Chi-restraints excluded: chain D residue  314 ARG
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  355 MET
Chi-restraints excluded: chain D residue  359 PHE
Chi-restraints excluded: chain E residue  314 ARG
Chi-restraints excluded: chain E residue  338 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 35 optimal weight:    6.9990
   chunk 61 optimal weight:    5.9990
   chunk 28 optimal weight:    0.2980
   chunk 24 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 79 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
D 121 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.112398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.084148 restraints weight = 20219.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 2.58
r_work: 0.2905 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.1387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  13085  Z= 0.117
  Angle     :  0.445   9.541  17685  Z= 0.234
  Chirality :  0.039   0.193   2050
  Planarity :  0.003   0.037   2235
  Dihedral  :  3.682  14.505   1720
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  :  9.89 %
    Favored  : 88.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.56 (0.21), residues: 1585
  helix:  2.92 (0.15), residues: 1090
  sheet:  2.02 (0.39), residues: 145
  loop :  0.63 (0.38), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 162 
 HIS   0.001   0.000   HIS C 122 
 PHE   0.020   0.001   PHE D 352 
 TYR   0.012   0.001   TYR E 299 
 ARG   0.004   0.000   ARG A 372 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04497 ( 1015)
  hydrogen bonds       : angle       3.78710 ( 2970)
  covalent geometry    : bond        0.00242 (13085)
  covalent geometry    : angle       0.44544 (17685)

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

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

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 165
  time to evaluate  : 1.403 
Fit side-chains
REVERT: A   94 GLN cc_start: 0.8221 (mp10) cc_final: 0.7757 (mp10)
REVERT: A  383 MET cc_start: 0.6886 (mmp) cc_final: 0.6219 (mtp)
REVERT: B  359 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.7472 (t80)
REVERT: C  124 MET cc_start: 0.8826 (tpt) cc_final: 0.8577 (tpp)
REVERT: C  383 MET cc_start: 0.6771 (mmp) cc_final: 0.6033 (mtm)
REVERT: D  359 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7716 (t80)
REVERT: D  383 MET cc_start: 0.6836 (mmp) cc_final: 0.6171 (mtp)
REVERT: E   94 GLN cc_start: 0.8248 (mp10) cc_final: 0.7744 (mp10)
REVERT: E  124 MET cc_start: 0.8869 (tpt) cc_final: 0.8548 (tpp)
REVERT: E  314 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7018 (mmp80)
REVERT: E  349 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8104 (mp)
REVERT: E  383 MET cc_start: 0.6814 (mmp) cc_final: 0.6016 (mtp)
  outliers start: 22
  outliers final: 10
  residues processed: 173
  average time/residue: 1.1684
  time to fit residues: 221.0335
Evaluate side-chains
  166 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 152
  time to evaluate  : 1.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  257 GLU
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain B residue  359 PHE
Chi-restraints excluded: chain C residue  197 ILE
Chi-restraints excluded: chain C residue  359 PHE
Chi-restraints excluded: chain D residue  197 ILE
Chi-restraints excluded: chain D residue  257 GLU
Chi-restraints excluded: chain D residue  314 ARG
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  355 MET
Chi-restraints excluded: chain D residue  359 PHE
Chi-restraints excluded: chain E residue  314 ARG
Chi-restraints excluded: chain E residue  338 LEU
Chi-restraints excluded: chain E residue  349 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 117 optimal weight:    2.9990
   chunk 116 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   chunk 134 optimal weight:    0.8980
   chunk 106 optimal weight:    0.9990
   chunk 20 optimal weight:   10.0000
   chunk 127 optimal weight:    0.0570
   chunk 40 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   chunk 149 optimal weight:    1.9990
   overall best weight:    0.6900

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

Flipped N/Q/H residues before XYZ refinement:
A 121 GLN
D 121 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.112667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.084465 restraints weight = 20033.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 2.57
r_work: 0.2909 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.1430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  13085  Z= 0.118
  Angle     :  0.436   5.304  17685  Z= 0.232
  Chirality :  0.038   0.155   2050
  Planarity :  0.003   0.037   2235
  Dihedral  :  3.664  14.592   1720
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 10.53 %
    Favored  : 88.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.61 (0.21), residues: 1585
  helix:  3.01 (0.15), residues: 1070
  sheet:  2.01 (0.39), residues: 145
  loop :  0.65 (0.37), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 162 
 HIS   0.002   0.000   HIS C 122 
 PHE   0.020   0.001   PHE D 352 
 TYR   0.015   0.001   TYR C 299 
 ARG   0.004   0.000   ARG A 372 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04470 ( 1015)
  hydrogen bonds       : angle       3.76143 ( 2970)
  covalent geometry    : bond        0.00245 (13085)
  covalent geometry    : angle       0.43583 (17685)

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

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

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 161
  time to evaluate  : 1.399 
Fit side-chains
REVERT: A   94 GLN cc_start: 0.8234 (mp10) cc_final: 0.7772 (mp10)
REVERT: A  381 MET cc_start: 0.6620 (ttm) cc_final: 0.6292 (mtp)
REVERT: A  383 MET cc_start: 0.6915 (mmp) cc_final: 0.6237 (mtp)
REVERT: B   94 GLN cc_start: 0.8150 (mp10) cc_final: 0.7591 (mp10)
REVERT: B  344 MET cc_start: 0.8641 (mtm) cc_final: 0.8427 (mtp)
REVERT: B  359 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.7482 (t80)
REVERT: C  124 MET cc_start: 0.8804 (tpt) cc_final: 0.8565 (tpp)
REVERT: C  383 MET cc_start: 0.6714 (mmp) cc_final: 0.5925 (mtm)
REVERT: D  359 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7627 (t80)
REVERT: D  383 MET cc_start: 0.6819 (mmp) cc_final: 0.6155 (mtp)
REVERT: E   94 GLN cc_start: 0.8246 (mp10) cc_final: 0.7741 (mp10)
REVERT: E  124 MET cc_start: 0.8826 (tpt) cc_final: 0.8515 (tpp)
REVERT: E  314 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7017 (mmp80)
REVERT: E  349 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8094 (mp)
REVERT: E  383 MET cc_start: 0.6740 (mmp) cc_final: 0.6002 (mtp)
  outliers start: 17
  outliers final: 7
  residues processed: 166
  average time/residue: 1.1772
  time to fit residues: 214.1243
Evaluate side-chains
  162 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 151
  time to evaluate  : 1.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  257 GLU
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain B residue  359 PHE
Chi-restraints excluded: chain C residue  197 ILE
Chi-restraints excluded: chain D residue  197 ILE
Chi-restraints excluded: chain D residue  314 ARG
Chi-restraints excluded: chain D residue  355 MET
Chi-restraints excluded: chain D residue  359 PHE
Chi-restraints excluded: chain E residue  314 ARG
Chi-restraints excluded: chain E residue  338 LEU
Chi-restraints excluded: chain E residue  349 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 93 optimal weight:    6.9990
   chunk 83 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9990
   chunk 124 optimal weight:    6.9990
   chunk 71 optimal weight:    1.9990
   chunk 95 optimal weight:    0.5980
   chunk 81 optimal weight:    4.9990
   chunk 123 optimal weight:    7.9990
   chunk 74 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0980
   chunk 118 optimal weight:    3.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 121 GLN
D 121 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.111521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.083194 restraints weight = 19808.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 2.52
r_work: 0.2951 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.1466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  13085  Z= 0.133
  Angle     :  0.460   9.955  17685  Z= 0.240
  Chirality :  0.039   0.146   2050
  Planarity :  0.003   0.037   2235
  Dihedral  :  3.700  14.506   1720
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 10.74 %
    Favored  : 88.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.57 (0.21), residues: 1585
  helix:  2.97 (0.15), residues: 1070
  sheet:  2.03 (0.39), residues: 145
  loop :  0.65 (0.37), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 162 
 HIS   0.002   0.000   HIS C 122 
 PHE   0.020   0.001   PHE E 352 
 TYR   0.017   0.001   TYR C 299 
 ARG   0.004   0.000   ARG C 372 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04588 ( 1015)
  hydrogen bonds       : angle       3.80338 ( 2970)
  covalent geometry    : bond        0.00288 (13085)
  covalent geometry    : angle       0.46003 (17685)

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

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

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 157
  time to evaluate  : 1.545 
Fit side-chains
REVERT: A   94 GLN cc_start: 0.8214 (mp10) cc_final: 0.7748 (mp10)
REVERT: A  381 MET cc_start: 0.6494 (ttm) cc_final: 0.6157 (mtp)
REVERT: A  383 MET cc_start: 0.6818 (mmp) cc_final: 0.6156 (mtp)
REVERT: B   94 GLN cc_start: 0.8180 (mp10) cc_final: 0.7617 (mp10)
REVERT: B  359 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7484 (t80)
REVERT: C  124 MET cc_start: 0.8776 (tpt) cc_final: 0.8526 (tpp)
REVERT: C  383 MET cc_start: 0.6659 (mmp) cc_final: 0.5899 (mtm)
REVERT: D  359 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7645 (t80)
REVERT: D  383 MET cc_start: 0.6748 (mmp) cc_final: 0.6087 (mtp)
REVERT: E   94 GLN cc_start: 0.8228 (mp10) cc_final: 0.7707 (mp10)
REVERT: E  314 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.6893 (mmp80)
REVERT: E  349 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7953 (mp)
REVERT: E  383 MET cc_start: 0.6729 (mmp) cc_final: 0.5944 (mtp)
  outliers start: 16
  outliers final: 8
  residues processed: 163
  average time/residue: 1.1638
  time to fit residues: 208.0734
Evaluate side-chains
  159 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 147
  time to evaluate  : 1.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  257 GLU
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain B residue  359 PHE
Chi-restraints excluded: chain C residue  197 ILE
Chi-restraints excluded: chain D residue  314 ARG
Chi-restraints excluded: chain D residue  355 MET
Chi-restraints excluded: chain D residue  359 PHE
Chi-restraints excluded: chain E residue  314 ARG
Chi-restraints excluded: chain E residue  338 LEU
Chi-restraints excluded: chain E residue  349 LEU
Chi-restraints excluded: chain E residue  395 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 131 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 144 optimal weight:    9.9990
   chunk 68 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 71 optimal weight:    0.0070
   chunk 79 optimal weight:    0.8980
   chunk 129 optimal weight:    0.5980
   chunk 125 optimal weight:    1.9990
   chunk 98 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9980
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
A 121 GLN
A 362 ASN
D 121 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.112537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.084337 restraints weight = 19968.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3077 rms_B_bonded: 2.58
r_work: 0.2906 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.1469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  13085  Z= 0.115
  Angle     :  0.443   9.849  17685  Z= 0.234
  Chirality :  0.038   0.151   2050
  Planarity :  0.003   0.037   2235
  Dihedral  :  3.647  14.688   1720
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 10.81 %
    Favored  : 88.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.62 (0.21), residues: 1585
  helix:  2.98 (0.15), residues: 1090
  sheet:  2.03 (0.39), residues: 145
  loop :  0.64 (0.38), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 162 
 HIS   0.001   0.000   HIS C 122 
 PHE   0.020   0.001   PHE D 352 
 TYR   0.017   0.001   TYR C 299 
 ARG   0.004   0.000   ARG C 372 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04450 ( 1015)
  hydrogen bonds       : angle       3.75091 ( 2970)
  covalent geometry    : bond        0.00235 (13085)
  covalent geometry    : angle       0.44292 (17685)

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

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

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 154
  time to evaluate  : 1.568 
Fit side-chains
REVERT: A   94 GLN cc_start: 0.8238 (mp10) cc_final: 0.7776 (mp10)
REVERT: A  381 MET cc_start: 0.6625 (ttm) cc_final: 0.6339 (mtp)
REVERT: A  383 MET cc_start: 0.6881 (mmp) cc_final: 0.6204 (mtp)
REVERT: B   94 GLN cc_start: 0.8165 (mp10) cc_final: 0.7608 (mp10)
REVERT: B  359 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7521 (t80)
REVERT: B  362 ASN cc_start: 0.7700 (m-40) cc_final: 0.7383 (m-40)
REVERT: C  124 MET cc_start: 0.8793 (tpt) cc_final: 0.8557 (tpp)
REVERT: C  383 MET cc_start: 0.6711 (mmp) cc_final: 0.5904 (mtm)
REVERT: D  359 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7697 (t80)
REVERT: D  383 MET cc_start: 0.6817 (mmp) cc_final: 0.6159 (mtp)
REVERT: E   94 GLN cc_start: 0.8257 (mp10) cc_final: 0.7754 (mp10)
REVERT: E  349 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8085 (mp)
REVERT: E  383 MET cc_start: 0.6844 (mmp) cc_final: 0.6080 (mtp)
  outliers start: 16
  outliers final: 9
  residues processed: 160
  average time/residue: 1.1250
  time to fit residues: 198.5075
Evaluate side-chains
  160 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 148
  time to evaluate  : 1.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain B residue  257 GLU
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain B residue  359 PHE
Chi-restraints excluded: chain C residue  197 ILE
Chi-restraints excluded: chain D residue  197 ILE
Chi-restraints excluded: chain D residue  314 ARG
Chi-restraints excluded: chain D residue  355 MET
Chi-restraints excluded: chain D residue  359 PHE
Chi-restraints excluded: chain E residue  338 LEU
Chi-restraints excluded: chain E residue  349 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 36 optimal weight:    0.0570
   chunk 32 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9990
   chunk 87 optimal weight:    0.7980
   chunk 40 optimal weight:   10.0000
   chunk 101 optimal weight:    0.5980
   chunk 116 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 56 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
A 362 ASN
D 121 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.113222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.085076 restraints weight = 19891.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 2.57
r_work: 0.2909 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.1499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  13085  Z= 0.112
  Angle     :  0.449  10.278  17685  Z= 0.235
  Chirality :  0.038   0.151   2050
  Planarity :  0.003   0.037   2235
  Dihedral  :  3.605  14.814   1720
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 10.81 %
    Favored  : 88.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.67 (0.21), residues: 1585
  helix:  3.01 (0.15), residues: 1090
  sheet:  2.03 (0.39), residues: 145
  loop :  0.67 (0.38), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 162 
 HIS   0.001   0.000   HIS C 122 
 PHE   0.020   0.001   PHE C 352 
 TYR   0.014   0.001   TYR D 299 
 ARG   0.004   0.000   ARG C 372 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04406 ( 1015)
  hydrogen bonds       : angle       3.72764 ( 2970)
  covalent geometry    : bond        0.00227 (13085)
  covalent geometry    : angle       0.44903 (17685)

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

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

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3170 Ramachandran restraints generated.
    1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 158
  time to evaluate  : 1.395 
Fit side-chains
REVERT: A   94 GLN cc_start: 0.8234 (mp10) cc_final: 0.7777 (mp10)
REVERT: A  381 MET cc_start: 0.6571 (ttm) cc_final: 0.6295 (mtp)
REVERT: A  383 MET cc_start: 0.6921 (mmp) cc_final: 0.6218 (mtp)
REVERT: B   94 GLN cc_start: 0.8182 (mp10) cc_final: 0.7628 (mp10)
REVERT: B  359 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7533 (t80)
REVERT: B  362 ASN cc_start: 0.7532 (m-40) cc_final: 0.7119 (m-40)
REVERT: C  124 MET cc_start: 0.8787 (tpt) cc_final: 0.8570 (tpp)
REVERT: C  383 MET cc_start: 0.6700 (mmp) cc_final: 0.5905 (mtm)
REVERT: D  359 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7741 (t80)
REVERT: D  383 MET cc_start: 0.6811 (mmp) cc_final: 0.6157 (mtp)
REVERT: E   94 GLN cc_start: 0.8270 (mp10) cc_final: 0.7807 (mp10)
REVERT: E  383 MET cc_start: 0.6774 (mmp) cc_final: 0.6046 (mtp)
  outliers start: 15
  outliers final: 9
  residues processed: 164
  average time/residue: 1.0872
  time to fit residues: 196.4156
Evaluate side-chains
  161 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 150
  time to evaluate  : 1.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain B residue  257 GLU
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain B residue  359 PHE
Chi-restraints excluded: chain C residue  197 ILE
Chi-restraints excluded: chain D residue  197 ILE
Chi-restraints excluded: chain D residue  314 ARG
Chi-restraints excluded: chain D residue  355 MET
Chi-restraints excluded: chain D residue  359 PHE
Chi-restraints excluded: chain E residue  338 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 118 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 122 optimal weight:    0.9990
   chunk 125 optimal weight:    4.9990
   chunk 25 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 107 optimal weight:    0.7980
   chunk 89 optimal weight:    7.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
D 121 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.112322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.084028 restraints weight = 19952.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 2.57
r_work: 0.2898 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  13085  Z= 0.128
  Angle     :  0.457   9.890  17685  Z= 0.241
  Chirality :  0.039   0.160   2050
  Planarity :  0.003   0.037   2235
  Dihedral  :  3.644  14.630   1720
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 11.02 %
    Favored  : 88.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.64 (0.21), residues: 1585
  helix:  2.99 (0.15), residues: 1090
  sheet:  2.00 (0.39), residues: 145
  loop :  0.67 (0.38), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 162 
 HIS   0.002   0.000   HIS C 122 
 PHE   0.029   0.001   PHE E 395 
 TYR   0.017   0.001   TYR C 299 
 ARG   0.004   0.000   ARG C 372 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04526 ( 1015)
  hydrogen bonds       : angle       3.76228 ( 2970)
  covalent geometry    : bond        0.00274 (13085)
  covalent geometry    : angle       0.45694 (17685)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7638.74 seconds
wall clock time: 132 minutes 30.36 seconds (7950.36 seconds total)