Starting phenix.real_space_refine
on Tue Mar  3 17:35:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x1r_32947/03_2026/7x1r_32947.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x1r_32947/03_2026/7x1r_32947.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x1r_32947/03_2026/7x1r_32947.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x1r_32947/03_2026/7x1r_32947.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x1r_32947/03_2026/7x1r_32947.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x1r_32947/03_2026/7x1r_32947.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Au      2     10.57       5
     P       4      5.49       5
     S      38      5.16       5
     C    4824      2.51       5
     N    1298      2.21       5
     O    1442      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 86 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7608
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 485, 3750
          Classifications: {'peptide': 485}
          Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 465}
    Chain: "A"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 54
          Unusual residues: {' AU': 1, 'FAD': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1419  SG  CYS A 189      73.629  62.408  61.033  1.00 28.54           S

  Restraints were copied for chains:
    B
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb="AU    AU A 502 " occ=0.30
    residue:
      pdb="AU    AU B 502 " occ=0.30
  Time building chain proxies: 2.69, per 1000 atoms: 0.35
  Number of scatterers: 7608
  At special positions: 0
  Unit cell: (116.8, 104, 76.8, 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)
     Au      2     78.96
     S      38     16.00
     P       4     15.00
     O    1442      8.00
     N    1298      7.00
     C    4824      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  59 " - pdb=" SG  CYS A  64 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  59 " - pdb=" SG  CYS B  64 " 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: 0.81
  Conformation dependent library (CDL) restraints added in 291.0 milliseconds
  

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1744

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 12 sheets defined
      36.7% alpha, 23.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 34
      removed outlier: 3.679A  pdb=" N   TYR A  34 " --> pdb=" O   GLU A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 63
      removed outlier: 4.346A  pdb=" N   VAL A  60 " --> pdb=" O   GLY A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 84
      removed outlier: 4.127A  pdb=" N   ARG A  84 " --> pdb=" O   LEU A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 123
    Processing helix  chain 'A' and resid 172 through 177
    Processing helix  chain 'A' and resid 180 through 184
      removed outlier: 4.188A  pdb=" N   PHE A 184 " --> pdb=" O   SER A 180 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 180 through 184'
    Processing helix  chain 'A' and resid 199 through 212
    Processing helix  chain 'A' and resid 229 through 243
    Processing helix  chain 'A' and resid 342 through 359
    Processing helix  chain 'A' and resid 386 through 395
    Processing helix  chain 'A' and resid 408 through 412
    Processing helix  chain 'A' and resid 430 through 432
      No H-bonds generated for 'chain 'A' and resid 430 through 432'
    Processing helix  chain 'A' and resid 444 through 458
      removed outlier: 4.208A  pdb=" N   GLY A 451 " --> pdb=" O   GLU A 447 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   PHE A 452 " --> pdb=" O   VAL A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 468
    Processing helix  chain 'A' and resid 474 through 481
    Processing helix  chain 'B' and resid 21 through 34
      removed outlier: 3.679A  pdb=" N   TYR B  34 " --> pdb=" O   GLU B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 63
      removed outlier: 4.347A  pdb=" N   VAL B  60 " --> pdb=" O   GLY B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 63 through 84
      removed outlier: 4.127A  pdb=" N   ARG B  84 " --> pdb=" O   LEU B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 123
    Processing helix  chain 'B' and resid 172 through 177
    Processing helix  chain 'B' and resid 180 through 184
      removed outlier: 4.188A  pdb=" N   PHE B 184 " --> pdb=" O   SER B 180 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 180 through 184'
    Processing helix  chain 'B' and resid 199 through 212
    Processing helix  chain 'B' and resid 229 through 243
    Processing helix  chain 'B' and resid 342 through 359
    Processing helix  chain 'B' and resid 386 through 395
    Processing helix  chain 'B' and resid 408 through 412
    Processing helix  chain 'B' and resid 430 through 432
      No H-bonds generated for 'chain 'B' and resid 430 through 432'
    Processing helix  chain 'B' and resid 444 through 458
      removed outlier: 4.208A  pdb=" N   GLY B 451 " --> pdb=" O   GLU B 447 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   PHE B 452 " --> pdb=" O   VAL B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 461 through 468
    Processing helix  chain 'B' and resid 474 through 481
    Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 128
      removed outlier: 7.235A  pdb=" N   MET A  39 " --> pdb=" O   TYR A  13 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   LEU A  15 " --> pdb=" O   MET A  39 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   LEU A  41 " --> pdb=" O   LEU A  15 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ILE A  17 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ASP A  14 " --> pdb=" O   ARG A 156 " (cutoff:3.500A)
      removed outlier: 7.770A  pdb=" N   LEU A 158 " --> pdb=" O   ASP A  14 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   ILE A  16 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   ARG A 139 " --> pdb=" O   ILE A 135 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ILE A 135 " --> pdb=" O   ARG A 139 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 128
      removed outlier: 7.235A  pdb=" N   MET A  39 " --> pdb=" O   TYR A  13 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   LEU A  15 " --> pdb=" O   MET A  39 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   LEU A  41 " --> pdb=" O   LEU A  15 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ILE A  17 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ASP A  14 " --> pdb=" O   ARG A 156 " (cutoff:3.500A)
      removed outlier: 7.770A  pdb=" N   LEU A 158 " --> pdb=" O   ASP A  14 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   ILE A  16 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
      removed outlier: 8.242A  pdb=" N   TYR A 330 " --> pdb=" O   GLU A 155 " (cutoff:3.500A)
      removed outlier: 6.101A  pdb=" N   PHE A 157 " --> pdb=" O   TYR A 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 165
    Processing sheet with id=AA4, first strand: chain 'A' and resid 178 through 179
      removed outlier: 6.828A  pdb=" N   ILE A 178 " --> pdb=" O   LEU A 289 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 251 through 260
      removed outlier: 5.997A  pdb=" N   GLN A 272 " --> pdb=" O   PRO A 253 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ARG A 266 " --> pdb=" O   ILE A 259 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 372 through 374
      removed outlier: 5.929A  pdb=" N   VAL A 435 " --> pdb=" O   ASN A 428 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   ASN A 428 " --> pdb=" O   VAL A 435 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 126 through 128
      removed outlier: 7.235A  pdb=" N   MET B  39 " --> pdb=" O   TYR B  13 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   LEU B  15 " --> pdb=" O   MET B  39 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   LEU B  41 " --> pdb=" O   LEU B  15 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ILE B  17 " --> pdb=" O   LEU B  41 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ASP B  14 " --> pdb=" O   ARG B 156 " (cutoff:3.500A)
      removed outlier: 7.771A  pdb=" N   LEU B 158 " --> pdb=" O   ASP B  14 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ILE B  16 " --> pdb=" O   LEU B 158 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   ARG B 139 " --> pdb=" O   ILE B 135 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE B 135 " --> pdb=" O   ARG B 139 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 126 through 128
      removed outlier: 7.235A  pdb=" N   MET B  39 " --> pdb=" O   TYR B  13 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   LEU B  15 " --> pdb=" O   MET B  39 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   LEU B  41 " --> pdb=" O   LEU B  15 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ILE B  17 " --> pdb=" O   LEU B  41 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ASP B  14 " --> pdb=" O   ARG B 156 " (cutoff:3.500A)
      removed outlier: 7.771A  pdb=" N   LEU B 158 " --> pdb=" O   ASP B  14 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ILE B  16 " --> pdb=" O   LEU B 158 " (cutoff:3.500A)
      removed outlier: 8.242A  pdb=" N   TYR B 330 " --> pdb=" O   GLU B 155 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   PHE B 157 " --> pdb=" O   TYR B 330 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 163 through 165
    Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 179
      removed outlier: 6.829A  pdb=" N   ILE B 178 " --> pdb=" O   LEU B 289 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 251 through 260
      removed outlier: 5.997A  pdb=" N   GLN B 272 " --> pdb=" O   PRO B 253 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   ARG B 266 " --> pdb=" O   ILE B 259 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 372 through 374
      removed outlier: 5.929A  pdb=" N   VAL B 435 " --> pdb=" O   ASN B 428 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   ASN B 428 " --> pdb=" O   VAL B 435 " (cutoff:3.500A)

    342 hydrogen bonds defined for protein.
    948 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: 1.36

  Time building geometry restraints manager: 1.06 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2486
        1.35 -     1.47: 1858
        1.47 -     1.60: 3368
        1.60 -     1.72: 0
        1.72 -     1.85: 52
  Bond restraints: 7764
  Sorted by residual:
  bond pdb=" O3P FAD B 501 "
       pdb=" P   FAD B 501 "
    ideal  model  delta    sigma   weight residual
    1.660  1.559  0.101 2.00e-02 2.50e+03 2.56e+01
  bond pdb=" O3P FAD A 501 "
       pdb=" P   FAD A 501 "
    ideal  model  delta    sigma   weight residual
    1.660  1.559  0.101 2.00e-02 2.50e+03 2.54e+01
  bond pdb=" O5B FAD A 501 "
       pdb=" PA  FAD A 501 "
    ideal  model  delta    sigma   weight residual
    1.634  1.557  0.077 2.00e-02 2.50e+03 1.49e+01
  bond pdb=" O5B FAD B 501 "
       pdb=" PA  FAD B 501 "
    ideal  model  delta    sigma   weight residual
    1.634  1.557  0.077 2.00e-02 2.50e+03 1.48e+01
  bond pdb=" O5' FAD A 501 "
       pdb=" P   FAD A 501 "
    ideal  model  delta    sigma   weight residual
    1.637  1.573  0.064 2.00e-02 2.50e+03 1.03e+01
  ... (remaining 7759 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 10120
        1.67 -     3.33: 354
        3.33 -     5.00: 33
        5.00 -     6.66: 21
        6.66 -     8.33: 4
  Bond angle restraints: 10532
  Sorted by residual:
  angle pdb=" N   VAL A 305 "
        pdb=" CA  VAL A 305 "
        pdb=" C   VAL A 305 "
      ideal   model   delta    sigma   weight residual
     113.47  109.63    3.84 1.01e+00 9.80e-01 1.45e+01
  angle pdb=" N   VAL B 305 "
        pdb=" CA  VAL B 305 "
        pdb=" C   VAL B 305 "
      ideal   model   delta    sigma   weight residual
     113.47  109.63    3.84 1.01e+00 9.80e-01 1.45e+01
  angle pdb=" C   GLY A 207 "
        pdb=" N   PHE A 208 "
        pdb=" CA  PHE A 208 "
      ideal   model   delta    sigma   weight residual
     121.14  115.43    5.71 1.75e+00 3.27e-01 1.06e+01
  angle pdb=" C   GLY B 207 "
        pdb=" N   PHE B 208 "
        pdb=" CA  PHE B 208 "
      ideal   model   delta    sigma   weight residual
     121.14  115.45    5.69 1.75e+00 3.27e-01 1.06e+01
  angle pdb=" C   ARG B 221 "
        pdb=" N   SER B 222 "
        pdb=" CA  SER B 222 "
      ideal   model   delta    sigma   weight residual
     122.17  117.21    4.96 1.54e+00 4.22e-01 1.04e+01
  ... (remaining 10527 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.52: 4241
       17.52 -    35.03: 327
       35.03 -    52.55: 66
       52.55 -    70.06: 16
       70.06 -    87.58: 16
  Dihedral angle restraints: 4666
    sinusoidal: 1912
      harmonic: 2754
  Sorted by residual:
  dihedral pdb=" CA  CYS A  59 "
           pdb=" CB  CYS A  59 "
           pdb=" SG  CYS A  59 "
           pdb=" SG  CYS A  64 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00    1.60  -74.60     1      2.00e+01 2.50e-03 1.76e+01
  dihedral pdb=" CA  CYS B  59 "
           pdb=" CB  CYS B  59 "
           pdb=" SG  CYS B  59 "
           pdb=" SG  CYS B  64 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00    1.55  -74.55     1      2.00e+01 2.50e-03 1.76e+01
  dihedral pdb=" CA  ALA B 160 "
           pdb=" C   ALA B 160 "
           pdb=" N   THR B 161 "
           pdb=" CA  THR B 161 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.97  -18.03     0      5.00e+00 4.00e-02 1.30e+01
  ... (remaining 4663 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 653
       0.034 -    0.068: 317
       0.068 -    0.102: 141
       0.102 -    0.136: 54
       0.136 -    0.169: 9
  Chirality restraints: 1174
  Sorted by residual:
  chirality pdb=" CA  PHE B 208 "
            pdb=" N   PHE B 208 "
            pdb=" C   PHE B 208 "
            pdb=" CB  PHE B 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.18e-01
  chirality pdb=" CA  PHE A 208 "
            pdb=" N   PHE A 208 "
            pdb=" C   PHE A 208 "
            pdb=" CB  PHE A 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.14e-01
  chirality pdb=" C2B FAD B 501 "
            pdb=" C1B FAD B 501 "
            pdb=" C3B FAD B 501 "
            pdb=" O2B FAD B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.70    0.16 2.00e-01 2.50e+01 6.67e-01
  ... (remaining 1171 not shown)

  Planarity restraints: 1336
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 170 "   -0.021 5.00e-02 4.00e+02   3.23e-02 1.67e+00
        pdb=" N   PRO B 171 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO B 171 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 171 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 170 "    0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO A 171 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 171 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 171 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 208 "    0.011 2.00e-02 2.50e+03   9.59e-03 1.61e+00
        pdb=" CG  PHE B 208 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 208 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 208 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 208 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 208 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 208 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1333 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 969
        2.74 -     3.28: 7362
        3.28 -     3.82: 12429
        3.82 -     4.36: 14855
        4.36 -     4.90: 25607
  Nonbonded interactions: 61222
  Sorted by model distance:
  nonbonded pdb=" SG  CYS B 189 "
            pdb="AU    AU B 502 "
     model   vdw
     2.205 2.980
  nonbonded pdb=" SG  CYS A 189 "
            pdb="AU    AU A 502 "
     model   vdw
     2.205 2.980
  nonbonded pdb=" O   LEU A  55 "
            pdb=" ND2 ASN A 113 "
     model   vdw
     2.207 3.120
  nonbonded pdb=" O   LEU B  55 "
            pdb=" ND2 ASN B 113 "
     model   vdw
     2.207 3.120
  nonbonded pdb=" OG1 THR B 324 "
            pdb=" O   ILE B 329 "
     model   vdw
     2.229 3.040
  ... (remaining 61217 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.30 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.050
  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:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.970
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
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      :  0.007   0.101   7766  Z= 0.334
  Angle     :  0.759   8.330  10536  Z= 0.415
  Chirality :  0.049   0.169   1174
  Planarity :  0.004   0.032   1336
  Dihedral  : 14.250  87.578   2916
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  7.02 %
    Favored  : 92.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.91 (0.24), residues: 966
  helix:  0.38 (0.27), residues: 290
  sheet: -0.35 (0.32), residues: 264
  loop : -1.43 (0.26), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 434 
 TYR   0.015   0.002   TYR B 200 
 PHE   0.022   0.003   PHE B 208 
 TRP   0.006   0.001   TRP B  53 
 HIS   0.005   0.002   HIS A  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00723 ( 7764)
  covalent geometry    : angle       0.75489 (10532)
  SS BOND              : bond        0.00484 (    2)
  SS BOND              : angle       3.94276 (    4)
  hydrogen bonds       : bond        0.13022 (  336)
  hydrogen bonds       : angle       7.38796 (  948)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 274
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A   25 LEU cc_start: 0.9068 (mt) cc_final: 0.8765 (mt)
REVERT: A   30 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6696 (mm-30)
REVERT: A   81 GLN cc_start: 0.8046 (tt0) cc_final: 0.7775 (tt0)
REVERT: A   85 ASN cc_start: 0.8597 (m110) cc_final: 0.8307 (m-40)
REVERT: A  139 ARG cc_start: 0.8374 (mtm110) cc_final: 0.7830 (mtp85)
REVERT: A  140 ILE cc_start: 0.8784 (pt) cc_final: 0.8417 (pt)
REVERT: A  222 SER cc_start: 0.8722 (p) cc_final: 0.8236 (t)
REVERT: A  308 LYS cc_start: 0.7831 (mttp) cc_final: 0.7470 (tttm)
REVERT: A  353 LEU cc_start: 0.9032 (tp) cc_final: 0.8722 (tp)
REVERT: A  396 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8136 (tm-30)
REVERT: A  397 GLU cc_start: 0.7204 (pt0) cc_final: 0.6684 (mt-10)
REVERT: A  450 GLN cc_start: 0.8872 (tp40) cc_final: 0.8586 (tp-100)
REVERT: B   85 ASN cc_start: 0.8572 (m110) cc_final: 0.8344 (m-40)
REVERT: B   93 THR cc_start: 0.8346 (t) cc_final: 0.8073 (p)
REVERT: B  192 LYS cc_start: 0.7898 (tttt) cc_final: 0.7443 (ttmm)
REVERT: B  222 SER cc_start: 0.8533 (p) cc_final: 0.8126 (t)
REVERT: B  252 VAL cc_start: 0.9108 (p) cc_final: 0.8897 (m)
REVERT: B  308 LYS cc_start: 0.7906 (mttp) cc_final: 0.7441 (tttm)
REVERT: B  396 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8203 (tm-30)
REVERT: B  397 GLU cc_start: 0.7089 (pt0) cc_final: 0.6762 (mt-10)
REVERT: B  425 ILE cc_start: 0.8854 (pt) cc_final: 0.8408 (mt)
REVERT: B  450 GLN cc_start: 0.8875 (tp40) cc_final: 0.8528 (tp-100)
  outliers start: 2
  outliers final: 2
  residues processed: 276
  average time/residue: 0.0965
  time to fit residues: 34.5233
Evaluate side-chains
  187 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 185
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain B residue  370 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    6.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN
** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 144 ASN
B 113 ASN
B 144 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.141018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.122318 restraints weight = 8925.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.124483 restraints weight = 6422.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.126124 restraints weight = 5036.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.127111 restraints weight = 4207.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.128010 restraints weight = 3706.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3291
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3291 r_free = 0.3291    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3291 r_free = 0.3291    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3291
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.2267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7766  Z= 0.139
  Angle     :  0.575   6.509  10536  Z= 0.306
  Chirality :  0.047   0.150   1174
  Planarity :  0.004   0.051   1336
  Dihedral  :  6.511  49.835   1148
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 15.04 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.26), residues: 966
  helix:  1.92 (0.29), residues: 294
  sheet:  0.07 (0.33), residues: 256
  loop : -1.12 (0.26), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 121 
 TYR   0.014   0.002   TYR B  13 
 PHE   0.025   0.002   PHE B 208 
 TRP   0.013   0.001   TRP B  98 
 HIS   0.006   0.002   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 7764)
  covalent geometry    : angle       0.57225 (10532)
  SS BOND              : bond        0.00387 (    2)
  SS BOND              : angle       2.99878 (    4)
  hydrogen bonds       : bond        0.04145 (  336)
  hydrogen bonds       : angle       5.87045 (  948)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 202
  time to evaluate  : 0.285 
Fit side-chains
REVERT: A   25 LEU cc_start: 0.9006 (mt) cc_final: 0.8687 (mt)
REVERT: A   49 LEU cc_start: 0.8559 (mp) cc_final: 0.8355 (mp)
REVERT: A  157 PHE cc_start: 0.8554 (m-80) cc_final: 0.8324 (m-10)
REVERT: A  222 SER cc_start: 0.8706 (p) cc_final: 0.8288 (t)
REVERT: A  308 LYS cc_start: 0.7938 (mttp) cc_final: 0.7478 (tttm)
REVERT: A  479 PHE cc_start: 0.8598 (m-80) cc_final: 0.8290 (m-80)
REVERT: B   29 LYS cc_start: 0.7941 (mtpt) cc_final: 0.7666 (mttt)
REVERT: B  139 ARG cc_start: 0.8292 (mtm110) cc_final: 0.7749 (mtp85)
REVERT: B  157 PHE cc_start: 0.8492 (m-80) cc_final: 0.8244 (m-10)
REVERT: B  192 LYS cc_start: 0.7890 (tttt) cc_final: 0.7538 (ttmm)
REVERT: B  222 SER cc_start: 0.8629 (p) cc_final: 0.8148 (t)
REVERT: B  252 VAL cc_start: 0.8867 (p) cc_final: 0.8654 (m)
REVERT: B  308 LYS cc_start: 0.7886 (mttp) cc_final: 0.7434 (tttm)
REVERT: B  386 SER cc_start: 0.8664 (t) cc_final: 0.8246 (p)
REVERT: B  450 GLN cc_start: 0.8716 (tp40) cc_final: 0.8344 (tp-100)
  outliers start: 15
  outliers final: 9
  residues processed: 213
  average time/residue: 0.0758
  time to fit residues: 22.4365
Evaluate side-chains
  189 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 180
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue  250 GLN
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 66 optimal weight:   10.0000
   chunk 45 optimal weight:    7.9990
   chunk 42 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 14 optimal weight:    5.9990
   chunk 52 optimal weight:    0.7980
   chunk 95 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 129 ASN
B 129 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.141927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.123388 restraints weight = 8867.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.125289 restraints weight = 7816.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.127221 restraints weight = 5731.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.127231 restraints weight = 4731.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.127506 restraints weight = 4418.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3290
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3290 r_free = 0.3290    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3290 r_free = 0.3290    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3290
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.2905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7766  Z= 0.121
  Angle     :  0.531   6.160  10536  Z= 0.282
  Chirality :  0.046   0.178   1174
  Planarity :  0.004   0.039   1336
  Dihedral  :  6.182  50.612   1148
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 16.17 %
    Favored  : 80.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.27), residues: 966
  helix:  2.43 (0.30), residues: 292
  sheet:  0.22 (0.32), residues: 256
  loop : -0.91 (0.27), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  84 
 TYR   0.011   0.001   TYR B  13 
 PHE   0.023   0.002   PHE A 208 
 TRP   0.003   0.001   TRP B  53 
 HIS   0.004   0.001   HIS B 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 7764)
  covalent geometry    : angle       0.52915 (10532)
  SS BOND              : bond        0.00417 (    2)
  SS BOND              : angle       2.36780 (    4)
  hydrogen bonds       : bond        0.03755 (  336)
  hydrogen bonds       : angle       5.53791 (  948)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 199
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A   39 MET cc_start: 0.8680 (ppp) cc_final: 0.8442 (ppp)
REVERT: A   49 LEU cc_start: 0.8698 (mp) cc_final: 0.8335 (mp)
REVERT: A  139 ARG cc_start: 0.8018 (mtm110) cc_final: 0.7569 (mtp85)
REVERT: A  222 SER cc_start: 0.8837 (p) cc_final: 0.8532 (t)
REVERT: A  308 LYS cc_start: 0.7992 (mttp) cc_final: 0.7487 (tttm)
REVERT: A  397 GLU cc_start: 0.7074 (pt0) cc_final: 0.6778 (mt-10)
REVERT: A  403 HIS cc_start: 0.8664 (p90) cc_final: 0.8311 (p-80)
REVERT: A  479 PHE cc_start: 0.8480 (m-80) cc_final: 0.8044 (m-80)
REVERT: B   15 LEU cc_start: 0.9265 (tp) cc_final: 0.8999 (tt)
REVERT: B  139 ARG cc_start: 0.8138 (mtm110) cc_final: 0.7646 (mtp85)
REVERT: B  222 SER cc_start: 0.8804 (p) cc_final: 0.8391 (t)
REVERT: B  252 VAL cc_start: 0.8706 (p) cc_final: 0.8408 (m)
REVERT: B  308 LYS cc_start: 0.7951 (mttp) cc_final: 0.7412 (tttm)
REVERT: B  397 GLU cc_start: 0.7280 (pt0) cc_final: 0.7051 (mt-10)
REVERT: B  425 ILE cc_start: 0.8529 (pt) cc_final: 0.8138 (mt)
  outliers start: 25
  outliers final: 20
  residues processed: 217
  average time/residue: 0.0778
  time to fit residues: 23.1204
Evaluate side-chains
  201 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 181
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASP
Chi-restraints excluded: chain A residue   64 CYS
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  250 GLN
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  426 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 4 optimal weight:    8.9990
   chunk 60 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 71 optimal weight:    7.9990
   chunk 77 optimal weight:    0.4980
   chunk 82 optimal weight:    6.9990
   chunk 3 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 14 optimal weight:    7.9990
   chunk 26 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    2.6986

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

Flipped N/Q/H residues before XYZ refinement:
** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.135589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.116654 restraints weight = 9254.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.118664 restraints weight = 6681.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.120180 restraints weight = 5258.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.121157 restraints weight = 4422.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.122073 restraints weight = 3914.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3221
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3221 r_free = 0.3221    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3221 r_free = 0.3221    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3221
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.3372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7766  Z= 0.199
  Angle     :  0.603   5.608  10536  Z= 0.316
  Chirality :  0.047   0.145   1174
  Planarity :  0.004   0.034   1336
  Dihedral  :  6.423  51.692   1148
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 17.67 %
    Favored  : 76.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.26), residues: 966
  helix:  2.46 (0.31), residues: 282
  sheet:  0.08 (0.32), residues: 258
  loop : -0.87 (0.27), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  84 
 TYR   0.013   0.002   TYR A 358 
 PHE   0.022   0.002   PHE B 208 
 TRP   0.005   0.001   TRP B  53 
 HIS   0.006   0.002   HIS B 243 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 7764)
  covalent geometry    : angle       0.60123 (10532)
  SS BOND              : bond        0.00525 (    2)
  SS BOND              : angle       2.21244 (    4)
  hydrogen bonds       : bond        0.04229 (  336)
  hydrogen bonds       : angle       5.61843 (  948)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 183
  time to evaluate  : 0.317 
Fit side-chains
REVERT: A   39 MET cc_start: 0.8767 (ppp) cc_final: 0.8538 (ppp)
REVERT: A   49 LEU cc_start: 0.8689 (mp) cc_final: 0.8477 (mp)
REVERT: A  222 SER cc_start: 0.9002 (p) cc_final: 0.8767 (t)
REVERT: A  308 LYS cc_start: 0.8154 (mttp) cc_final: 0.7503 (tttm)
REVERT: A  403 HIS cc_start: 0.8630 (p90) cc_final: 0.8040 (p90)
REVERT: B  139 ARG cc_start: 0.8100 (mtm110) cc_final: 0.7650 (mtp85)
REVERT: B  205 CYS cc_start: 0.8193 (m) cc_final: 0.7991 (m)
REVERT: B  222 SER cc_start: 0.8981 (p) cc_final: 0.8625 (t)
REVERT: B  289 LEU cc_start: 0.9080 (mt) cc_final: 0.8669 (mp)
REVERT: B  308 LYS cc_start: 0.8093 (mttp) cc_final: 0.7478 (tttm)
REVERT: B  397 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6951 (mt-10)
  outliers start: 44
  outliers final: 33
  residues processed: 214
  average time/residue: 0.0752
  time to fit residues: 22.5240
Evaluate side-chains
  205 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 171
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASP
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  192 LYS
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  250 GLN
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  392 GLU
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  480 THR
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 25 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   chunk 60 optimal weight:    6.9990
   chunk 77 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 24 optimal weight:    6.9990
   chunk 79 optimal weight:    0.0980
   chunk 51 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    2.4186

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

Flipped N/Q/H residues before XYZ refinement:
** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 243 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.135775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.118835 restraints weight = 9159.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.119154 restraints weight = 6581.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.119557 restraints weight = 5761.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.119785 restraints weight = 5557.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.120046 restraints weight = 5124.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3192
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3192
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.3733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7766  Z= 0.179
  Angle     :  0.584   6.478  10536  Z= 0.306
  Chirality :  0.046   0.149   1174
  Planarity :  0.004   0.031   1336
  Dihedral  :  6.327  52.171   1148
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 20.68 %
    Favored  : 73.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.26), residues: 966
  helix:  2.44 (0.31), residues: 280
  sheet: -0.12 (0.31), residues: 258
  loop : -0.82 (0.27), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  84 
 TYR   0.012   0.001   TYR A 358 
 PHE   0.023   0.002   PHE B 208 
 TRP   0.004   0.001   TRP B  88 
 HIS   0.005   0.002   HIS A 472 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 7764)
  covalent geometry    : angle       0.58216 (10532)
  SS BOND              : bond        0.00746 (    2)
  SS BOND              : angle       2.38254 (    4)
  hydrogen bonds       : bond        0.03974 (  336)
  hydrogen bonds       : angle       5.65116 (  948)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 189
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 LEU cc_start: 0.9323 (mp) cc_final: 0.8976 (mm)
REVERT: A  205 CYS cc_start: 0.8061 (m) cc_final: 0.7739 (m)
REVERT: A  222 SER cc_start: 0.9079 (p) cc_final: 0.8795 (t)
REVERT: A  308 LYS cc_start: 0.8193 (mttp) cc_final: 0.7758 (tttm)
REVERT: A  403 HIS cc_start: 0.8576 (p90) cc_final: 0.8042 (p90)
REVERT: B  101 MET cc_start: 0.8586 (ttm) cc_final: 0.8109 (ttp)
REVERT: B  139 ARG cc_start: 0.8084 (mtm110) cc_final: 0.7666 (mtp85)
REVERT: B  222 SER cc_start: 0.9066 (p) cc_final: 0.8758 (t)
REVERT: B  308 LYS cc_start: 0.8194 (mttp) cc_final: 0.7583 (tttm)
REVERT: B  433 GLU cc_start: 0.8445 (mp0) cc_final: 0.8036 (pm20)
  outliers start: 45
  outliers final: 34
  residues processed: 220
  average time/residue: 0.0702
  time to fit residues: 21.9560
Evaluate side-chains
  210 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 176
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASP
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  192 LYS
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  250 GLN
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  480 THR
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 40 optimal weight:    0.7980
   chunk 48 optimal weight:   10.0000
   chunk 16 optimal weight:    9.9990
   chunk 15 optimal weight:    0.0970
   chunk 28 optimal weight:    1.9990
   chunk 69 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 144 ASN
B 243 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.138407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.121454 restraints weight = 9119.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.121551 restraints weight = 8522.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.122346 restraints weight = 7615.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.122701 restraints weight = 6223.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.123098 restraints weight = 5700.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3234
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3234 r_free = 0.3234    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3235 r_free = 0.3235    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3235
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.3999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7766  Z= 0.115
  Angle     :  0.536   6.320  10536  Z= 0.282
  Chirality :  0.045   0.146   1174
  Planarity :  0.004   0.033   1336
  Dihedral  :  6.139  53.902   1148
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 22.06 %
    Favored  : 73.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.27), residues: 966
  helix:  2.52 (0.31), residues: 282
  sheet:  0.01 (0.32), residues: 244
  loop : -0.67 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  84 
 TYR   0.011   0.001   TYR B  13 
 PHE   0.027   0.002   PHE B 208 
 TRP   0.007   0.001   TRP B 407 
 HIS   0.012   0.002   HIS B 243 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 7764)
  covalent geometry    : angle       0.53400 (10532)
  SS BOND              : bond        0.00221 (    2)
  SS BOND              : angle       2.56768 (    4)
  hydrogen bonds       : bond        0.03510 (  336)
  hydrogen bonds       : angle       5.43291 (  948)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 192
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 LEU cc_start: 0.9213 (mp) cc_final: 0.8843 (mm)
REVERT: A  139 ARG cc_start: 0.7961 (mtm110) cc_final: 0.7541 (mtp85)
REVERT: A  149 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6385 (tm-30)
REVERT: A  222 SER cc_start: 0.9053 (p) cc_final: 0.8824 (t)
REVERT: A  308 LYS cc_start: 0.8095 (mttp) cc_final: 0.7593 (tmtt)
REVERT: A  479 PHE cc_start: 0.8645 (m-80) cc_final: 0.8197 (m-80)
REVERT: B   76 LEU cc_start: 0.9229 (mp) cc_final: 0.8858 (mm)
REVERT: B  139 ARG cc_start: 0.8075 (mtm110) cc_final: 0.7651 (mtp85)
REVERT: B  222 SER cc_start: 0.9040 (p) cc_final: 0.8792 (t)
  outliers start: 33
  outliers final: 28
  residues processed: 213
  average time/residue: 0.0673
  time to fit residues: 20.2320
Evaluate side-chains
  211 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 182
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASP
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 69 optimal weight:    7.9990
   chunk 94 optimal weight:    3.9990
   chunk 44 optimal weight:    0.8980
   chunk 78 optimal weight:    6.9990
   chunk 9 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 63 optimal weight:    7.9990
   chunk 49 optimal weight:    9.9990
   chunk 15 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 444 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.138674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.120092 restraints weight = 9001.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.120801 restraints weight = 8592.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.122045 restraints weight = 7026.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.122448 restraints weight = 5689.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.122600 restraints weight = 5270.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3226
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3226
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.4160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7766  Z= 0.127
  Angle     :  0.554   6.956  10536  Z= 0.289
  Chirality :  0.045   0.156   1174
  Planarity :  0.004   0.035   1336
  Dihedral  :  6.103  53.283   1148
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 23.18 %
    Favored  : 72.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.27), residues: 966
  helix:  2.55 (0.31), residues: 284
  sheet: -0.09 (0.31), residues: 258
  loop : -0.77 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  84 
 TYR   0.015   0.001   TYR A  13 
 PHE   0.030   0.002   PHE A 208 
 TRP   0.005   0.001   TRP B  88 
 HIS   0.005   0.001   HIS A 243 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 7764)
  covalent geometry    : angle       0.55205 (10532)
  SS BOND              : bond        0.00188 (    2)
  SS BOND              : angle       2.30336 (    4)
  hydrogen bonds       : bond        0.03493 (  336)
  hydrogen bonds       : angle       5.37853 (  948)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 201
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 LEU cc_start: 0.9206 (mp) cc_final: 0.8834 (mm)
REVERT: A  140 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8071 (pt)
REVERT: A  222 SER cc_start: 0.9085 (p) cc_final: 0.8833 (t)
REVERT: A  308 LYS cc_start: 0.8115 (mttp) cc_final: 0.7563 (tmtt)
REVERT: A  403 HIS cc_start: 0.8569 (p90) cc_final: 0.8084 (p90)
REVERT: A  479 PHE cc_start: 0.8631 (m-80) cc_final: 0.8315 (m-80)
REVERT: B   76 LEU cc_start: 0.9243 (mp) cc_final: 0.8872 (mm)
REVERT: B  139 ARG cc_start: 0.8335 (mtm110) cc_final: 0.7657 (mtp85)
REVERT: B  222 SER cc_start: 0.9112 (p) cc_final: 0.8908 (t)
REVERT: B  308 LYS cc_start: 0.8188 (mttp) cc_final: 0.7556 (tmtt)
REVERT: B  366 ASP cc_start: 0.7121 (t0) cc_final: 0.6800 (t0)
  outliers start: 32
  outliers final: 26
  residues processed: 221
  average time/residue: 0.0679
  time to fit residues: 21.2144
Evaluate side-chains
  219 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 192
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASP
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  332 ILE
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 60 optimal weight:    6.9990
   chunk 67 optimal weight:    0.7980
   chunk 17 optimal weight:    6.9990
   chunk 82 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9980
   chunk 15 optimal weight:    0.4980
   chunk 84 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 94 optimal weight:    3.9990
   chunk 56 optimal weight:    0.6980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 239 HIS
A 243 HIS
** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 444 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.140801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.123146 restraints weight = 9038.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.123280 restraints weight = 8825.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.123846 restraints weight = 7963.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.124398 restraints weight = 6578.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.124966 restraints weight = 5756.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3256
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3256 r_free = 0.3256    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3256 r_free = 0.3256    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3256
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.4351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7766  Z= 0.114
  Angle     :  0.561  10.305  10536  Z= 0.290
  Chirality :  0.046   0.245   1174
  Planarity :  0.004   0.033   1336
  Dihedral  :  6.001  51.957   1148
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 23.81 %
    Favored  : 72.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.69 (0.27), residues: 966
  helix:  2.58 (0.31), residues: 284
  sheet:  0.08 (0.32), residues: 244
  loop : -0.74 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  84 
 TYR   0.010   0.001   TYR B  13 
 PHE   0.029   0.002   PHE B 208 
 TRP   0.004   0.001   TRP B  88 
 HIS   0.005   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 7764)
  covalent geometry    : angle       0.55857 (10532)
  SS BOND              : bond        0.00064 (    2)
  SS BOND              : angle       2.64120 (    4)
  hydrogen bonds       : bond        0.03276 (  336)
  hydrogen bonds       : angle       5.26139 (  948)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 200
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A   67 LYS cc_start: 0.9020 (tmmt) cc_final: 0.8788 (tttt)
REVERT: A   76 LEU cc_start: 0.9186 (mp) cc_final: 0.8809 (mm)
REVERT: A   86 TYR cc_start: 0.8849 (m-80) cc_final: 0.8483 (m-80)
REVERT: A  139 ARG cc_start: 0.7919 (mtm110) cc_final: 0.7506 (mtp85)
REVERT: A  150 LYS cc_start: 0.8052 (mtmt) cc_final: 0.7598 (tptp)
REVERT: A  308 LYS cc_start: 0.8112 (mttp) cc_final: 0.7577 (tmtt)
REVERT: A  362 THR cc_start: 0.7767 (m) cc_final: 0.7257 (t)
REVERT: A  366 ASP cc_start: 0.7207 (t0) cc_final: 0.6922 (t0)
REVERT: A  403 HIS cc_start: 0.8641 (p90) cc_final: 0.8228 (p90)
REVERT: A  479 PHE cc_start: 0.8546 (m-80) cc_final: 0.8210 (m-80)
REVERT: B   76 LEU cc_start: 0.9247 (mp) cc_final: 0.8798 (mm)
REVERT: B  139 ARG cc_start: 0.8353 (mtm110) cc_final: 0.7653 (mtp85)
REVERT: B  308 LYS cc_start: 0.8176 (mttp) cc_final: 0.7580 (tmtt)
REVERT: B  353 LEU cc_start: 0.8951 (tp) cc_final: 0.8737 (tp)
REVERT: B  366 ASP cc_start: 0.7078 (t0) cc_final: 0.6789 (t0)
REVERT: B  403 HIS cc_start: 0.8420 (p90) cc_final: 0.8100 (p90)
  outliers start: 31
  outliers final: 24
  residues processed: 221
  average time/residue: 0.0764
  time to fit residues: 23.6398
Evaluate side-chains
  218 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 194
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  245 ILE
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 52 optimal weight:    7.9990
   chunk 12 optimal weight:    2.9990
   chunk 69 optimal weight:   10.0000
   chunk 88 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 23 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 243 HIS
** A 403 HIS ** 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 = 0.3415 r_free = 0.3415 target = 0.138495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.120353 restraints weight = 9162.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.120200 restraints weight = 9441.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.121076 restraints weight = 8272.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.121490 restraints weight = 6718.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.121754 restraints weight = 6039.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3216
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3216 r_free = 0.3216    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3216 r_free = 0.3216    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3216
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.4397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7766  Z= 0.152
  Angle     :  0.612  12.890  10536  Z= 0.314
  Chirality :  0.046   0.161   1174
  Planarity :  0.004   0.051   1336
  Dihedral  :  6.123  52.709   1148
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 23.68 %
    Favored  : 72.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.27), residues: 966
  helix:  2.47 (0.31), residues: 284
  sheet: -0.02 (0.32), residues: 244
  loop : -0.76 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B  84 
 TYR   0.012   0.001   TYR B  13 
 PHE   0.025   0.002   PHE B 208 
 TRP   0.006   0.001   TRP B  88 
 HIS   0.007   0.002   HIS A 243 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 7764)
  covalent geometry    : angle       0.60582 (10532)
  SS BOND              : bond        0.00161 (    2)
  SS BOND              : angle       4.58809 (    4)
  hydrogen bonds       : bond        0.03591 (  336)
  hydrogen bonds       : angle       5.34976 (  948)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 204
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LEU cc_start: 0.9225 (mp) cc_final: 0.8811 (mm)
REVERT: A   86 TYR cc_start: 0.8918 (m-80) cc_final: 0.8507 (m-80)
REVERT: A  139 ARG cc_start: 0.8026 (mtm110) cc_final: 0.7559 (mtp85)
REVERT: A  150 LYS cc_start: 0.8017 (mtmt) cc_final: 0.7500 (tptp)
REVERT: A  308 LYS cc_start: 0.8137 (mttp) cc_final: 0.7636 (tmtt)
REVERT: A  362 THR cc_start: 0.7788 (m) cc_final: 0.7367 (t)
REVERT: A  366 ASP cc_start: 0.7243 (t0) cc_final: 0.6962 (t0)
REVERT: A  403 HIS cc_start: 0.8547 (p90) cc_final: 0.8070 (p90)
REVERT: A  479 PHE cc_start: 0.8634 (m-80) cc_final: 0.8358 (m-80)
REVERT: B   76 LEU cc_start: 0.9310 (mp) cc_final: 0.8927 (mm)
REVERT: B   86 TYR cc_start: 0.8913 (m-80) cc_final: 0.8558 (m-80)
REVERT: B  139 ARG cc_start: 0.7986 (mtm110) cc_final: 0.7618 (mtp85)
REVERT: B  308 LYS cc_start: 0.8185 (mttp) cc_final: 0.7578 (tmtt)
REVERT: B  366 ASP cc_start: 0.7096 (t0) cc_final: 0.6880 (t0)
REVERT: B  425 ILE cc_start: 0.8597 (pt) cc_final: 0.8364 (mt)
  outliers start: 33
  outliers final: 28
  residues processed: 225
  average time/residue: 0.0666
  time to fit residues: 21.0811
Evaluate side-chains
  225 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 197
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  332 ILE
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 95 optimal weight:    0.3980
   chunk 27 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9990
   chunk 88 optimal weight:    0.0770
   chunk 56 optimal weight:    2.9990
   chunk 3 optimal weight:    7.9990
   chunk 92 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 83 optimal weight:    9.9990
   overall best weight:    0.8742

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
A 239 HIS
A 243 HIS
** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 444 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.140183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.122432 restraints weight = 8974.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.122546 restraints weight = 9647.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.123001 restraints weight = 8122.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.123547 restraints weight = 6890.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.124208 restraints weight = 6178.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3249
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3249 r_free = 0.3249    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3249 r_free = 0.3249    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3249
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.4536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7766  Z= 0.124
  Angle     :  0.592  12.690  10536  Z= 0.307
  Chirality :  0.046   0.156   1174
  Planarity :  0.004   0.050   1336
  Dihedral  :  6.031  52.141   1148
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 24.94 %
    Favored  : 71.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.27), residues: 966
  helix:  2.49 (0.31), residues: 286
  sheet: -0.13 (0.31), residues: 258
  loop : -0.71 (0.29), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B  84 
 TYR   0.013   0.001   TYR A  13 
 PHE   0.028   0.002   PHE B 208 
 TRP   0.005   0.001   TRP B 407 
 HIS   0.012   0.002   HIS A 243 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 7764)
  covalent geometry    : angle       0.58974 (10532)
  SS BOND              : bond        0.00079 (    2)
  SS BOND              : angle       2.71296 (    4)
  hydrogen bonds       : bond        0.03330 (  336)
  hydrogen bonds       : angle       5.39678 (  948)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 190
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 LEU cc_start: 0.9318 (mp) cc_final: 0.8837 (mm)
REVERT: A   86 TYR cc_start: 0.8866 (m-80) cc_final: 0.8482 (m-80)
REVERT: A  150 LYS cc_start: 0.7986 (mtmt) cc_final: 0.7514 (tptp)
REVERT: A  308 LYS cc_start: 0.8101 (mttp) cc_final: 0.7567 (tmtt)
REVERT: A  362 THR cc_start: 0.7700 (m) cc_final: 0.7206 (t)
REVERT: A  366 ASP cc_start: 0.7160 (t0) cc_final: 0.6901 (t0)
REVERT: A  403 HIS cc_start: 0.8508 (p90) cc_final: 0.8066 (p90)
REVERT: A  479 PHE cc_start: 0.8543 (m-80) cc_final: 0.8211 (m-80)
REVERT: B   76 LEU cc_start: 0.9249 (mp) cc_final: 0.8831 (mm)
REVERT: B   86 TYR cc_start: 0.8774 (m-80) cc_final: 0.8305 (m-80)
REVERT: B  139 ARG cc_start: 0.8252 (mtm110) cc_final: 0.7638 (mtp85)
REVERT: B  308 LYS cc_start: 0.8183 (mttp) cc_final: 0.7570 (tmtt)
REVERT: B  362 THR cc_start: 0.7686 (m) cc_final: 0.7090 (t)
REVERT: B  425 ILE cc_start: 0.8580 (pt) cc_final: 0.8363 (mt)
  outliers start: 27
  outliers final: 27
  residues processed: 208
  average time/residue: 0.0632
  time to fit residues: 18.9561
Evaluate side-chains
  212 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 185
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  475 CYS
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 63 optimal weight:    0.0770
   chunk 44 optimal weight:    4.9990
   chunk 69 optimal weight:   10.0000
   chunk 11 optimal weight:    6.9990
   chunk 39 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 71 optimal weight:    7.9990
   chunk 1 optimal weight:    9.9990
   chunk 72 optimal weight:    8.9990
   overall best weight:    1.9744

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

Flipped N/Q/H residues before XYZ refinement:
A 239 HIS
A 243 HIS
** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 403 HIS ** 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 = 0.3407 r_free = 0.3407 target = 0.137754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.120364 restraints weight = 9087.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.120354 restraints weight = 8708.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.121002 restraints weight = 7807.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.121365 restraints weight = 6596.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.121604 restraints weight = 6031.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3215
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3215
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.4565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7766  Z= 0.163
  Angle     :  0.611  12.647  10536  Z= 0.317
  Chirality :  0.046   0.158   1174
  Planarity :  0.004   0.053   1336
  Dihedral  :  6.240  53.577   1148
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 24.69 %
    Favored  : 71.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.27), residues: 966
  helix:  2.42 (0.31), residues: 284
  sheet: -0.22 (0.31), residues: 258
  loop : -0.76 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  84 
 TYR   0.012   0.001   TYR A  13 
 PHE   0.024   0.002   PHE B 208 
 TRP   0.006   0.001   TRP B  88 
 HIS   0.006   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 7764)
  covalent geometry    : angle       0.61006 (10532)
  SS BOND              : bond        0.00260 (    2)
  SS BOND              : angle       1.79610 (    4)
  hydrogen bonds       : bond        0.03636 (  336)
  hydrogen bonds       : angle       5.43687 (  948)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1197.06 seconds
wall clock time: 21 minutes 25.39 seconds (1285.39 seconds total)