Starting phenix.real_space_refine
on Thu Mar 13 19:47:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k6n_36924/03_2025/8k6n_36924.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k6n_36924/03_2025/8k6n_36924.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k6n_36924/03_2025/8k6n_36924.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k6n_36924/03_2025/8k6n_36924.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k6n_36924/03_2025/8k6n_36924.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k6n_36924/03_2025/8k6n_36924.cif"
  }
  resolution = 3.2
  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=   0.002 sd=   0.029
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: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C    5915      2.51       5
     N    1575      2.21       5
     O    1741      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9291
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1807
          Classifications: {'peptide': 225}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 2611
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2611
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
    Chain: "C"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "D"
      Number of atoms: 267
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 267
          Classifications: {'peptide': 31}
          Link IDs: {'PTRANS': 3, 'TRANS': 27}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 2387
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 301, 2387
          Classifications: {'peptide': 301}
          Link IDs: {'PTRANS': 10, 'TRANS': 290}
    Chain: "S"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1783
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
  Time building chain proxies: 5.71, per 1000 atoms: 0.61
  Number of scatterers: 9291
  At special positions: 0
  Unit cell: (136, 123.25, 105.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      60     16.00
     O    1741      8.00
     N    1575      7.00
     C    5915      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 123 " - pdb=" SG  CYS E 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.04

  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: 2.35
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2224

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 16 sheets defined
      37.6% alpha, 20.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 30
      removed outlier: 3.778A  pdb=" N   LYS A  17 " --> pdb=" O   ALA A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 44
      No H-bonds generated for 'chain 'A' and resid 42 through 44'
    Processing helix  chain 'A' and resid 45 through 57
    Processing helix  chain 'A' and resid 208 through 212
      removed outlier: 3.589A  pdb=" N   LYS A 211 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   TRP A 212 " --> pdb=" O   ARG A 209 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 208 through 212'
    Processing helix  chain 'A' and resid 213 through 217
    Processing helix  chain 'A' and resid 243 through 256
      removed outlier: 3.984A  pdb=" N   LYS A 249 " --> pdb=" O   HIS A 245 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ASN A 256 " --> pdb=" O   ASP A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 282
    Processing helix  chain 'A' and resid 296 through 310
      removed outlier: 3.960A  pdb=" N   TYR A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ILE A 304 " --> pdb=" O   ALA A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 352
      removed outlier: 3.674A  pdb=" N   GLN A 334 " --> pdb=" O   THR A 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 7 through 23
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 45 through 48
      removed outlier: 3.964A  pdb=" N   ASP C  48 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 45 through 48'
    Processing helix  chain 'D' and resid 16 through 32
    Processing helix  chain 'E' and resid 46 through 78
      removed outlier: 3.786A  pdb=" N   PHE E  78 " --> pdb=" O   VAL E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 83 through 114
      removed outlier: 4.183A  pdb=" N   LEU E 104 " --> pdb=" O   ASN E 100 " (cutoff:3.500A)
      Proline residue:  E 105  - end of helix
    Processing helix  chain 'E' and resid 119 through 153
      Proline residue:  E 127  - end of helix
    Processing helix  chain 'E' and resid 161 through 180
    Processing helix  chain 'E' and resid 180 through 186
      removed outlier: 4.237A  pdb=" N   ALA E 184 " --> pdb=" O   ALA E 180 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 213 through 228
      removed outlier: 4.520A  pdb=" N   THR E 217 " --> pdb=" O   SER E 213 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 228 through 248
    Processing helix  chain 'E' and resid 256 through 281
      removed outlier: 3.976A  pdb=" N   HIS E 260 " --> pdb=" O   ASN E 256 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLN E 261 " --> pdb=" O   ASP E 257 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   LYS E 265 " --> pdb=" O   GLN E 261 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   THR E 266 " --> pdb=" O   ARG E 262 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   VAL E 274 " --> pdb=" O   LEU E 270 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   TRP E 281 " --> pdb=" O   PHE E 277 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 281 through 292
      removed outlier: 3.994A  pdb=" N   HIS E 285 " --> pdb=" O   TRP E 281 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 302 through 316
    Processing helix  chain 'E' and resid 316 through 327
      Proline residue:  E 322  - end of helix
    Processing helix  chain 'E' and resid 329 through 339
    Processing helix  chain 'S' and resid 28 through 32
      removed outlier: 3.559A  pdb=" N   PHE S  32 " --> pdb=" O   PHE S  29 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.637A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191
      removed outlier: 3.850A  pdb=" N   ALA A 221 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   CYS A 225 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 7.489A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 7.772A  pdb=" N   ASN A 270 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   VAL A 226 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 234 through 235
      removed outlier: 6.154A  pdb=" N   MET A 241 " --> pdb=" O   LEU A 235 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.844A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 62
      removed outlier: 3.663A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 105
      removed outlier: 6.394A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 153
      removed outlier: 3.536A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.866A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.046A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.262A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 4.235A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.885A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLY B 288 " --> pdb=" O   SER B 275 " (cutoff:3.500A)
      removed outlier: 7.359A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 5.554A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ASP B 303 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 188 through 194
      removed outlier: 4.060A  pdb=" N   GLU E 188 " --> pdb=" O   THR E 204 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   THR E 204 " --> pdb=" O   GLU E 188 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB3, first strand: chain 'S' and resid 58 through 60
      removed outlier: 6.612A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ALA S  92 " --> pdb=" O   LEU S 117 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 71 through 73
    Processing sheet with id=AB5, first strand: chain 'S' and resid 155 through 160
    Processing sheet with id=AB6, first strand: chain 'S' and resid 155 through 160
      removed outlier: 3.860A  pdb=" N   ALA S 211 " --> pdb=" O   SER S 208 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   SER S 208 " --> pdb=" O   ALA S 211 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'S' and resid 194 through 195
      removed outlier: 5.824A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)

    450 hydrogen bonds defined for protein.
    1293 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: 2.61

  Time building geometry restraints manager: 2.66 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2716
        1.33 -     1.46: 2118
        1.46 -     1.58: 4561
        1.58 -     1.70: 1
        1.70 -     1.83: 88
  Bond restraints: 9484
  Sorted by residual:
  bond pdb=" CA  SER D  22 "
       pdb=" CB  SER D  22 "
    ideal  model  delta    sigma   weight residual
    1.529  1.488  0.041 1.55e-02 4.16e+03 6.89e+00
  bond pdb=" N   SER D   3 "
       pdb=" CA  SER D   3 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.19e-02 7.06e+03 6.69e+00
  bond pdb=" CA  SER D   3 "
       pdb=" CB  SER D   3 "
    ideal  model  delta    sigma   weight residual
    1.530  1.493  0.037 1.50e-02 4.44e+03 6.20e+00
  bond pdb=" CB  PRO C  60 "
       pdb=" CG  PRO C  60 "
    ideal  model  delta    sigma   weight residual
    1.492  1.608 -0.116 5.00e-02 4.00e+02 5.42e+00
  bond pdb=" N   LYS D   4 "
       pdb=" CA  LYS D   4 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.45e-02 4.76e+03 5.34e+00
  ... (remaining 9479 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 12389
        1.56 -     3.12: 363
        3.12 -     4.68: 68
        4.68 -     6.24: 22
        6.24 -     7.80: 5
  Bond angle restraints: 12847
  Sorted by residual:
  angle pdb=" CA  PRO C  60 "
        pdb=" N   PRO C  60 "
        pdb=" CD  PRO C  60 "
      ideal   model   delta    sigma   weight residual
     112.00  104.94    7.06 1.40e+00 5.10e-01 2.54e+01
  angle pdb=" C   LYS E 268 "
        pdb=" N   MET E 269 "
        pdb=" CA  MET E 269 "
      ideal   model   delta    sigma   weight residual
     121.14  113.34    7.80 1.75e+00 3.27e-01 1.99e+01
  angle pdb=" N   ILE D  28 "
        pdb=" CA  ILE D  28 "
        pdb=" C   ILE D  28 "
      ideal   model   delta    sigma   weight residual
     110.62  106.62    4.00 1.02e+00 9.61e-01 1.54e+01
  angle pdb=" CA  ASN D  29 "
        pdb=" C   ASN D  29 "
        pdb=" O   ASN D  29 "
      ideal   model   delta    sigma   weight residual
     120.82  116.92    3.90 1.05e+00 9.07e-01 1.38e+01
  angle pdb=" CA  ARG D  35 "
        pdb=" C   ARG D  35 "
        pdb=" O   ARG D  35 "
      ideal   model   delta    sigma   weight residual
     120.70  116.90    3.80 1.08e+00 8.57e-01 1.24e+01
  ... (remaining 12842 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.31: 5107
       17.31 -    34.62: 440
       34.62 -    51.94: 80
       51.94 -    69.25: 9
       69.25 -    86.56: 6
  Dihedral angle restraints: 5642
    sinusoidal: 2195
      harmonic: 3447
  Sorted by residual:
  dihedral pdb=" CB  CYS S 159 "
           pdb=" SG  CYS S 159 "
           pdb=" SG  CYS S 229 "
           pdb=" CB  CYS S 229 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   60.52   32.48     1      1.00e+01 1.00e-02 1.50e+01
  dihedral pdb=" CA  PHE A 268 "
           pdb=" C   PHE A 268 "
           pdb=" N   LEU A 269 "
           pdb=" CA  LEU A 269 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.12   16.88     0      5.00e+00 4.00e-02 1.14e+01
  dihedral pdb=" CA  GLY S  26 "
           pdb=" C   GLY S  26 "
           pdb=" N   PHE S  27 "
           pdb=" CA  PHE S  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.74  -16.26     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 5639 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 1248
       0.063 -    0.126: 194
       0.126 -    0.189: 14
       0.189 -    0.252: 8
       0.252 -    0.316: 2
  Chirality restraints: 1466
  Sorted by residual:
  chirality pdb=" CA  TYR D  27 "
            pdb=" N   TYR D  27 "
            pdb=" C   TYR D  27 "
            pdb=" CB  TYR D  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.49e+00
  chirality pdb=" CA  ARG D  35 "
            pdb=" N   ARG D  35 "
            pdb=" C   ARG D  35 "
            pdb=" CB  ARG D  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CA  ILE D  31 "
            pdb=" N   ILE D  31 "
            pdb=" C   ILE D  31 "
            pdb=" CB  ILE D  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.24 2.00e-01 2.50e+01 1.45e+00
  ... (remaining 1463 not shown)

  Planarity restraints: 1618
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C  59 "    0.033 5.00e-02 4.00e+02   4.76e-02 3.62e+00
        pdb=" N   PRO C  60 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO C  60 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C  60 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP S 111 "   -0.012 2.00e-02 2.50e+03   1.14e-02 3.22e+00
        pdb=" CG  TRP S 111 "    0.031 2.00e-02 2.50e+03
        pdb=" CD1 TRP S 111 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP S 111 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP S 111 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP S 111 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP S 111 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP S 111 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP S 111 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP S 111 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER E 251 "   -0.028 5.00e-02 4.00e+02   4.22e-02 2.85e+00
        pdb=" N   PRO E 252 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO E 252 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO E 252 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1615 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1038
        2.75 -     3.29: 9080
        3.29 -     3.82: 14961
        3.82 -     4.36: 16897
        4.36 -     4.90: 29865
  Nonbonded interactions: 71841
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG E 263 "
            pdb=" OG1 THR E 266 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" O   HIS B  54 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" O   CYS A 255 "
            pdb=" NZ  LYS A 318 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" OG1 THR E  44 "
            pdb=" O   LYS E 301 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" NE  ARG S  67 "
            pdb=" OG1 THR S  84 "
     model   vdw
     2.238 3.120
  ... (remaining 71836 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             1.030
  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:          0.420
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.190
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6578
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   0.116   9484  Z= 0.262
  Angle     :  0.662   7.797  12847  Z= 0.384
  Chirality :  0.048   0.316   1466
  Planarity :  0.004   0.048   1618
  Dihedral  : 13.234  86.559   3412
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.79 %
    Favored  : 99.12 %
  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:  0.15 (0.25), residues: 1168
  helix:  1.96 (0.26), residues: 408
  sheet: -0.15 (0.32), residues: 273
  loop : -1.39 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP S 111 
 HIS   0.007   0.001   HIS D  26 
 PHE   0.018   0.002   PHE B 235 
 TYR   0.027   0.002   TYR D  27 
 ARG   0.002   0.000   ARG D  33 

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 162
  time to evaluate  : 1.147 
Fit side-chains
REVERT: A  262 ASP cc_start: 0.6790 (t0) cc_final: 0.6548 (t0)
REVERT: B   66 ASP cc_start: 0.8367 (p0) cc_final: 0.7777 (p0)
REVERT: E  107 THR cc_start: 0.8108 (m) cc_final: 0.7899 (m)
REVERT: E  226 ILE cc_start: 0.8028 (tp) cc_final: 0.7760 (tp)
REVERT: E  248 ASN cc_start: 0.6941 (m-40) cc_final: 0.6582 (m-40)
REVERT: E  267 THR cc_start: 0.7508 (m) cc_final: 0.7307 (m)
  outliers start: 1
  outliers final: 1
  residues processed: 162
  average time/residue: 0.2605
  time to fit residues: 57.7095
Evaluate side-chains
  154 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 153
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   34 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 91 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0970
   chunk 55 optimal weight:    2.9990
   chunk 68 optimal weight:    0.7980
   chunk 106 optimal weight:    9.9990
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 340 ASN
E 329 ASN
S 142 GLN
** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.172817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.142027 restraints weight = 13016.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3849 rms_B_bonded: 2.45
r_work: 0.3723 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6854
moved from start:          0.0876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   9484  Z= 0.239
  Angle     :  0.616  10.121  12847  Z= 0.320
  Chirality :  0.043   0.164   1466
  Planarity :  0.004   0.041   1618
  Dihedral  :  5.088  87.185   1284
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  :  9.22 %
    Favored  : 89.21 %
  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:  0.23 (0.25), residues: 1168
  helix:  2.13 (0.26), residues: 419
  sheet: -0.24 (0.31), residues: 276
  loop : -1.46 (0.27), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 169 
 HIS   0.004   0.001   HIS D  26 
 PHE   0.015   0.002   PHE B 235 
 TYR   0.029   0.002   TYR D  27 
 ARG   0.004   0.000   ARG S  38 

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 156
  time to evaluate  : 1.033 
Fit side-chains
   revert: symmetry clash
REVERT: A  262 ASP cc_start: 0.7302 (t0) cc_final: 0.7046 (t0)
REVERT: B  340 ASN cc_start: 0.7612 (t0) cc_final: 0.7323 (t0)
REVERT: E  179 LEU cc_start: 0.7488 (tp) cc_final: 0.7206 (tt)
REVERT: E  226 ILE cc_start: 0.8214 (tp) cc_final: 0.7883 (tp)
REVERT: E  248 ASN cc_start: 0.7239 (m-40) cc_final: 0.6875 (m-40)
REVERT: S  140 MET cc_start: 0.5236 (mtp) cc_final: 0.4847 (mtp)
  outliers start: 16
  outliers final: 12
  residues processed: 161
  average time/residue: 0.2269
  time to fit residues: 49.8647
Evaluate side-chains
  168 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 156
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain E residue   70 LEU
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain E residue  279 VAL
Chi-restraints excluded: chain E residue  318 THR
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  178 LEU
Chi-restraints excluded: chain S residue  187 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 50 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 60 optimal weight:    4.9990
   chunk 80 optimal weight:    1.9990
   chunk 113 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0970
   chunk 90 optimal weight:    2.9990
   chunk 89 optimal weight:    5.9990
   chunk 82 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
D  26 HIS
** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.171672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.140940 restraints weight = 13061.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.3830 rms_B_bonded: 2.45
r_work: 0.3702 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6888
moved from start:          0.1178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9484  Z= 0.260
  Angle     :  0.600   7.720  12847  Z= 0.316
  Chirality :  0.043   0.165   1466
  Planarity :  0.004   0.040   1618
  Dihedral  :  5.078  88.212   1281
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 12.46 %
    Favored  : 84.99 %
  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:  0.24 (0.25), residues: 1168
  helix:  2.27 (0.26), residues: 411
  sheet: -0.34 (0.30), residues: 288
  loop : -1.46 (0.27), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 169 
 HIS   0.008   0.001   HIS D  26 
 PHE   0.017   0.002   PHE B 235 
 TYR   0.020   0.002   TYR D  27 
 ARG   0.002   0.000   ARG S  38 

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 159
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  262 ASP cc_start: 0.7303 (t0) cc_final: 0.7013 (t0)
REVERT: E  153 VAL cc_start: 0.8200 (p) cc_final: 0.7929 (m)
REVERT: E  226 ILE cc_start: 0.8280 (tp) cc_final: 0.7916 (tp)
REVERT: E  248 ASN cc_start: 0.7270 (m-40) cc_final: 0.6914 (m-40)
REVERT: E  328 MET cc_start: 0.6062 (tmm) cc_final: 0.5828 (tmm)
  outliers start: 26
  outliers final: 21
  residues processed: 170
  average time/residue: 0.2211
  time to fit residues: 51.6184
Evaluate side-chains
  178 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 157
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  277 GLU
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain E residue   70 LEU
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain E residue  279 VAL
Chi-restraints excluded: chain E residue  318 THR
Chi-restraints excluded: chain E residue  329 ASN
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  178 LEU
Chi-restraints excluded: chain S residue  187 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0270
   chunk 2 optimal weight:    1.9990
   chunk 104 optimal weight:    0.0670
   chunk 57 optimal weight:    8.9990
   chunk 101 optimal weight:    0.5980
   chunk 95 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 98 optimal weight:    3.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
D  26 HIS
** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.172756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.142143 restraints weight = 13076.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3851 rms_B_bonded: 2.47
r_work: 0.3725 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6854
moved from start:          0.1384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9484  Z= 0.194
  Angle     :  0.560   6.589  12847  Z= 0.295
  Chirality :  0.041   0.141   1466
  Planarity :  0.004   0.036   1618
  Dihedral  :  4.977  88.995   1281
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 15.60 %
    Favored  : 82.34 %
  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:  0.29 (0.25), residues: 1168
  helix:  2.29 (0.26), residues: 417
  sheet: -0.30 (0.31), residues: 280
  loop : -1.47 (0.27), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 332 
 HIS   0.008   0.001   HIS D  26 
 PHE   0.013   0.001   PHE A 190 
 TYR   0.018   0.001   TYR D  27 
 ARG   0.001   0.000   ARG S  38 

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 156
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  262 ASP cc_start: 0.7207 (t0) cc_final: 0.6920 (t0)
REVERT: C   44 HIS cc_start: 0.8043 (m90) cc_final: 0.7792 (m-70)
REVERT: D   32 THR cc_start: 0.7720 (OUTLIER) cc_final: 0.7424 (t)
REVERT: E  153 VAL cc_start: 0.8206 (p) cc_final: 0.7877 (m)
REVERT: E  226 ILE cc_start: 0.8234 (tp) cc_final: 0.7865 (tp)
REVERT: E  248 ASN cc_start: 0.7162 (m-40) cc_final: 0.6817 (m-40)
REVERT: E  328 MET cc_start: 0.5885 (tmm) cc_final: 0.5517 (tmm)
  outliers start: 21
  outliers final: 17
  residues processed: 164
  average time/residue: 0.2174
  time to fit residues: 49.2657
Evaluate side-chains
  170 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 152
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  277 GLU
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain D residue   32 THR
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain E residue  270 LEU
Chi-restraints excluded: chain E residue  279 VAL
Chi-restraints excluded: chain E residue  329 ASN
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  178 LEU
Chi-restraints excluded: chain S residue  187 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 26 optimal weight:    0.0050
   chunk 1 optimal weight:    0.5980
   chunk 110 optimal weight:    3.9990
   chunk 23 optimal weight:   20.0000
   chunk 79 optimal weight:    0.0980
   chunk 58 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0370
   chunk 43 optimal weight:    0.9990
   chunk 11 optimal weight:    4.9990
   chunk 18 optimal weight:    0.6980
   chunk 36 optimal weight:    0.0570
   overall best weight:    0.1590

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

Flipped N/Q/H residues before XYZ refinement:
D  26 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.175796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.145426 restraints weight = 13166.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3896 rms_B_bonded: 2.48
r_work: 0.3774 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6781
moved from start:          0.1651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9484  Z= 0.136
  Angle     :  0.535   6.933  12847  Z= 0.280
  Chirality :  0.040   0.126   1466
  Planarity :  0.003   0.034   1618
  Dihedral  :  4.791  87.887   1281
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 17.08 %
    Favored  : 80.37 %
  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:  0.46 (0.26), residues: 1168
  helix:  2.37 (0.26), residues: 417
  sheet: -0.26 (0.31), residues: 288
  loop : -1.27 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP S 111 
 HIS   0.006   0.001   HIS D  26 
 PHE   0.013   0.001   PHE E 319 
 TYR   0.016   0.001   TYR D  27 
 ARG   0.003   0.000   ARG E 187 

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 158
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  262 ASP cc_start: 0.7141 (t0) cc_final: 0.6840 (t0)
REVERT: D   32 THR cc_start: 0.7650 (OUTLIER) cc_final: 0.7354 (t)
REVERT: E  226 ILE cc_start: 0.8116 (tp) cc_final: 0.7732 (tp)
REVERT: E  328 MET cc_start: 0.5794 (tmm) cc_final: 0.5302 (tmm)
REVERT: E  329 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.8025 (m-40)
REVERT: S  187 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8248 (tp)
  outliers start: 26
  outliers final: 15
  residues processed: 172
  average time/residue: 0.1996
  time to fit residues: 47.9428
Evaluate side-chains
  176 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 158
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain D residue   21 TYR
Chi-restraints excluded: chain D residue   32 THR
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain E residue  270 LEU
Chi-restraints excluded: chain E residue  329 ASN
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  187 LEU
Chi-restraints excluded: chain S residue  188 LEU
Chi-restraints excluded: chain S residue  195 LEU
Chi-restraints excluded: chain S residue  226 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 107 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 108 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   chunk 80 optimal weight:    6.9990
   chunk 102 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 75 optimal weight:    4.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
D  26 HIS
** E  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.168589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.137913 restraints weight = 13063.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.3798 rms_B_bonded: 2.48
r_work: 0.3665 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6964
moved from start:          0.1791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.082   9484  Z= 0.485
  Angle     :  0.713  10.793  12847  Z= 0.376
  Chirality :  0.048   0.199   1466
  Planarity :  0.005   0.039   1618
  Dihedral  :  5.327  85.729   1281
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 17.37 %
    Favored  : 79.20 %
  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: -0.04 (0.25), residues: 1168
  helix:  1.96 (0.26), residues: 411
  sheet: -0.20 (0.31), residues: 272
  loop : -1.72 (0.26), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP B 169 
 HIS   0.011   0.002   HIS E 149 
 PHE   0.027   0.003   PHE A 337 
 TYR   0.034   0.003   TYR B 105 
 ARG   0.005   0.001   ARG B 314 

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 158
  time to evaluate  : 1.239 
Fit side-chains
REVERT: A  262 ASP cc_start: 0.7258 (t0) cc_final: 0.6953 (t0)
REVERT: B  118 ASP cc_start: 0.8085 (t0) cc_final: 0.7764 (t0)
REVERT: B  298 ASP cc_start: 0.7478 (t0) cc_final: 0.7094 (t0)
REVERT: D   32 THR cc_start: 0.7787 (OUTLIER) cc_final: 0.7512 (t)
REVERT: E   69 SER cc_start: 0.8227 (m) cc_final: 0.8006 (m)
REVERT: E  226 ILE cc_start: 0.8330 (tp) cc_final: 0.7968 (tp)
REVERT: E  248 ASN cc_start: 0.7286 (m-40) cc_final: 0.7026 (m-40)
REVERT: E  328 MET cc_start: 0.6046 (tmm) cc_final: 0.5624 (tmm)
  outliers start: 35
  outliers final: 25
  residues processed: 173
  average time/residue: 0.2320
  time to fit residues: 56.7506
Evaluate side-chains
  182 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 156
  time to evaluate  : 1.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain D residue   32 THR
Chi-restraints excluded: chain E residue   70 LEU
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue  279 VAL
Chi-restraints excluded: chain E residue  318 THR
Chi-restraints excluded: chain E residue  329 ASN
Chi-restraints excluded: chain S residue   37 VAL
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  187 LEU
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  195 LEU
Chi-restraints excluded: chain S residue  226 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9990
   chunk 95 optimal weight:    3.9990
   chunk 59 optimal weight:    7.9990
   chunk 34 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0970
   chunk 16 optimal weight:    0.3980
   chunk 108 optimal weight:    0.0270
   chunk 71 optimal weight:    1.9990
   chunk 83 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9990
   overall best weight:    0.4036

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  26 HIS
D  29 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.174495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.143966 restraints weight = 13150.330|
|-----------------------------------------------------------------------------|
r_work (start): 0.3864 rms_B_bonded: 2.50
r_work: 0.3734 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6857
moved from start:          0.1799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9484  Z= 0.168
  Angle     :  0.582   9.439  12847  Z= 0.301
  Chirality :  0.041   0.165   1466
  Planarity :  0.004   0.043   1618
  Dihedral  :  4.939  85.749   1281
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 19.53 %
    Favored  : 77.92 %
  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:  0.28 (0.25), residues: 1168
  helix:  2.31 (0.27), residues: 411
  sheet: -0.37 (0.31), residues: 275
  loop : -1.39 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.006   0.001   HIS D  26 
 PHE   0.014   0.001   PHE E 319 
 TYR   0.014   0.001   TYR S 102 
 ARG   0.003   0.000   ARG B 314 

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 159
  time to evaluate  : 0.953 
Fit side-chains
REVERT: A  262 ASP cc_start: 0.7151 (t0) cc_final: 0.6839 (t0)
REVERT: A  341 THR cc_start: 0.8106 (m) cc_final: 0.7872 (m)
REVERT: B  298 ASP cc_start: 0.7355 (t0) cc_final: 0.6998 (t0)
REVERT: C   46 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8675 (mtpt)
REVERT: D   32 THR cc_start: 0.7702 (OUTLIER) cc_final: 0.7463 (t)
REVERT: E  226 ILE cc_start: 0.8163 (tp) cc_final: 0.7790 (tp)
REVERT: E  248 ASN cc_start: 0.7011 (m-40) cc_final: 0.6752 (m-40)
REVERT: E  328 MET cc_start: 0.5866 (tmm) cc_final: 0.5319 (tmm)
REVERT: E  329 ASN cc_start: 0.8494 (OUTLIER) cc_final: 0.8049 (m-40)
  outliers start: 26
  outliers final: 16
  residues processed: 171
  average time/residue: 0.2380
  time to fit residues: 56.1538
Evaluate side-chains
  175 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 156
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain C residue   46 LYS
Chi-restraints excluded: chain D residue   32 THR
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain E residue  270 LEU
Chi-restraints excluded: chain E residue  329 ASN
Chi-restraints excluded: chain S residue   37 VAL
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  187 LEU
Chi-restraints excluded: chain S residue  195 LEU
Chi-restraints excluded: chain S residue  226 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 113 optimal weight:    0.0170
   chunk 14 optimal weight:    0.9990
   chunk 35 optimal weight:    0.3980
   chunk 103 optimal weight:    5.9990
   chunk 87 optimal weight:    0.7980
   chunk 107 optimal weight:    0.3980
   chunk 7 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.4418

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
D  26 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.174137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.143516 restraints weight = 13277.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.3865 rms_B_bonded: 2.52
r_work: 0.3734 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6846
moved from start:          0.1925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9484  Z= 0.165
  Angle     :  0.589   9.501  12847  Z= 0.300
  Chirality :  0.041   0.132   1466
  Planarity :  0.004   0.038   1618
  Dihedral  :  4.827  84.855   1281
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 20.31 %
    Favored  : 77.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.41 (0.26), residues: 1168
  helix:  2.41 (0.27), residues: 411
  sheet: -0.34 (0.31), residues: 282
  loop : -1.28 (0.28), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 332 
 HIS   0.006   0.001   HIS D  26 
 PHE   0.013   0.001   PHE E 319 
 TYR   0.014   0.001   TYR S 102 
 ARG   0.006   0.000   ARG E 187 

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 153
  time to evaluate  : 1.018 
Fit side-chains
REVERT: A  262 ASP cc_start: 0.7159 (t0) cc_final: 0.6835 (t0)
REVERT: B  118 ASP cc_start: 0.8006 (t0) cc_final: 0.7647 (t0)
REVERT: B  298 ASP cc_start: 0.7310 (t0) cc_final: 0.6949 (t0)
REVERT: D   32 THR cc_start: 0.7691 (OUTLIER) cc_final: 0.7452 (t)
REVERT: E  226 ILE cc_start: 0.8180 (tp) cc_final: 0.7800 (tp)
REVERT: E  328 MET cc_start: 0.5890 (tmm) cc_final: 0.5393 (tmm)
REVERT: E  329 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.8036 (m-40)
REVERT: S  187 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8239 (tp)
  outliers start: 21
  outliers final: 14
  residues processed: 162
  average time/residue: 0.2383
  time to fit residues: 53.3932
Evaluate side-chains
  167 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 150
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain D residue   32 THR
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain E residue  270 LEU
Chi-restraints excluded: chain E residue  329 ASN
Chi-restraints excluded: chain S residue   37 VAL
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  187 LEU
Chi-restraints excluded: chain S residue  195 LEU
Chi-restraints excluded: chain S residue  226 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 110 optimal weight:    0.2980
   chunk 27 optimal weight:    1.9990
   chunk 86 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 94 optimal weight:    4.9990
   chunk 96 optimal weight:    2.9990
   chunk 62 optimal weight:    8.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  26 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.171073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.140243 restraints weight = 13057.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.3830 rms_B_bonded: 2.50
r_work: 0.3697 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6893
moved from start:          0.1916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9484  Z= 0.241
  Angle     :  0.632  11.006  12847  Z= 0.324
  Chirality :  0.043   0.150   1466
  Planarity :  0.004   0.040   1618
  Dihedral  :  4.909  82.597   1281
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 20.71 %
    Favored  : 77.33 %
  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:  0.28 (0.25), residues: 1168
  helix:  2.30 (0.27), residues: 411
  sheet: -0.39 (0.31), residues: 276
  loop : -1.37 (0.27), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 169 
 HIS   0.007   0.001   HIS D  26 
 PHE   0.017   0.002   PHE B 235 
 TYR   0.022   0.002   TYR B 105 
 ARG   0.005   0.000   ARG A  32 

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 152
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
REVERT: A  262 ASP cc_start: 0.7194 (t0) cc_final: 0.6887 (t0)
REVERT: B  298 ASP cc_start: 0.7412 (t0) cc_final: 0.7059 (t0)
REVERT: D   32 THR cc_start: 0.7737 (OUTLIER) cc_final: 0.7501 (t)
REVERT: E  226 ILE cc_start: 0.8222 (tp) cc_final: 0.7849 (tp)
REVERT: E  328 MET cc_start: 0.5939 (tmm) cc_final: 0.5471 (tmm)
REVERT: E  329 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.8096 (m-40)
  outliers start: 20
  outliers final: 15
  residues processed: 161
  average time/residue: 0.2068
  time to fit residues: 46.6725
Evaluate side-chains
  169 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 152
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain D residue   32 THR
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain E residue  270 LEU
Chi-restraints excluded: chain E residue  329 ASN
Chi-restraints excluded: chain S residue   37 VAL
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  187 LEU
Chi-restraints excluded: chain S residue  195 LEU
Chi-restraints excluded: chain S residue  226 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 103 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 62 optimal weight:    8.9990
   chunk 84 optimal weight:    0.5980
   chunk 23 optimal weight:   20.0000
   chunk 6 optimal weight:    0.4980
   chunk 47 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 110 optimal weight:    4.9990
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
D  26 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.169770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.138888 restraints weight = 13203.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3795 rms_B_bonded: 2.51
r_work: 0.3662 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6941
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   9484  Z= 0.345
  Angle     :  0.685  10.678  12847  Z= 0.355
  Chirality :  0.046   0.191   1466
  Planarity :  0.004   0.041   1618
  Dihedral  :  5.111  77.930   1281
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 20.71 %
    Favored  : 77.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.07 (0.25), residues: 1168
  helix:  2.04 (0.27), residues: 410
  sheet: -0.32 (0.31), residues: 277
  loop : -1.53 (0.26), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP B 169 
 HIS   0.007   0.001   HIS E 149 
 PHE   0.021   0.002   PHE B 235 
 TYR   0.036   0.002   TYR B 105 
 ARG   0.009   0.000   ARG A  32 

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 161
  time to evaluate  : 1.390 
Fit side-chains
   revert: symmetry clash
REVERT: A  262 ASP cc_start: 0.7170 (t0) cc_final: 0.6836 (t0)
REVERT: B  118 ASP cc_start: 0.8100 (t0) cc_final: 0.7825 (t0)
REVERT: B  298 ASP cc_start: 0.7459 (t0) cc_final: 0.7102 (t0)
REVERT: D   32 THR cc_start: 0.7825 (OUTLIER) cc_final: 0.7603 (t)
REVERT: E   69 SER cc_start: 0.8191 (m) cc_final: 0.7972 (m)
REVERT: E  226 ILE cc_start: 0.8278 (tp) cc_final: 0.7904 (tp)
REVERT: E  328 MET cc_start: 0.6099 (tmm) cc_final: 0.5596 (tmm)
REVERT: E  329 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.8074 (m-40)
  outliers start: 23
  outliers final: 20
  residues processed: 170
  average time/residue: 0.2481
  time to fit residues: 58.5477
Evaluate side-chains
  181 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 159
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain D residue   32 THR
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain E residue  270 LEU
Chi-restraints excluded: chain E residue  279 VAL
Chi-restraints excluded: chain E residue  329 ASN
Chi-restraints excluded: chain S residue   37 VAL
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  187 LEU
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  195 LEU
Chi-restraints excluded: chain S residue  226 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 96 optimal weight:    5.9990
   chunk 32 optimal weight:    0.3980
   chunk 42 optimal weight:    3.9990
   chunk 86 optimal weight:    0.3980
   chunk 30 optimal weight:    0.9980
   chunk 77 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
D  26 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.168851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.138074 restraints weight = 13097.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.3800 rms_B_bonded: 2.47
r_work: 0.3670 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6921
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.104   9484  Z= 0.311
  Angle     :  0.946  59.194  12847  Z= 0.554
  Chirality :  0.043   0.176   1466
  Planarity :  0.005   0.051   1618
  Dihedral  :  5.170  77.993   1281
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 20.51 %
    Favored  : 76.94 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.05 (0.25), residues: 1168
  helix:  2.03 (0.26), residues: 410
  sheet: -0.34 (0.31), residues: 277
  loop : -1.53 (0.26), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 169 
 HIS   0.006   0.001   HIS D  26 
 PHE   0.020   0.002   PHE B 235 
 TYR   0.032   0.002   TYR B 105 
 ARG   0.008   0.000   ARG A  32 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8670.98 seconds
wall clock time: 151 minutes 25.95 seconds (9085.95 seconds total)