Starting phenix.real_space_refine
on Tue Mar  3 17:42:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7e7z_31005/03_2026/7e7z_31005.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7e7z_31005/03_2026/7e7z_31005.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7e7z_31005/03_2026/7e7z_31005.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7e7z_31005/03_2026/7e7z_31005.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7e7z_31005/03_2026/7e7z_31005.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7e7z_31005/03_2026/7e7z_31005.map"
  }
  resolution = 3.2
  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=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    5152      2.51       5
     N    1264      2.21       5
     O    1336      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 7808
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 248, 1952
          Classifications: {'peptide': 248}
          Link IDs: {'PTRANS': 8, 'TRANS': 239}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 248, 1952
          Classifications: {'peptide': 248}
          Link IDs: {'PTRANS': 8, 'TRANS': 239}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 248, 1952
          Classifications: {'peptide': 248}
          Link IDs: {'PTRANS': 8, 'TRANS': 239}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 248, 1952
          Classifications: {'peptide': 248}
          Link IDs: {'PTRANS': 8, 'TRANS': 239}
          Chain breaks: 1
  Time building chain proxies: 1.80, per 1000 atoms: 0.23
  Number of scatterers: 7808
  At special positions: 0
  Unit cell: (111.251, 111.251, 78.1763, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      56     16.00
     O    1336      8.00
     N    1264      7.00
     C    5152      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 334.3 milliseconds
  

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1880

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 0 sheets defined
      82.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 166 through 177
      removed outlier: 4.277A  pdb=" N   ARG A 170 " --> pdb=" O   THR A 166 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   ALA A 174 " --> pdb=" O   ARG A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 207
    Processing helix  chain 'A' and resid 227 through 249
    Processing helix  chain 'A' and resid 253 through 260
    Processing helix  chain 'A' and resid 260 through 282
      Proline residue:  A 272  - end of helix
      removed outlier: 3.769A  pdb=" N   ASN A 282 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 296
      removed outlier: 4.115A  pdb=" N   VAL A 290 " --> pdb=" O   SER A 286 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   THR A 291 " --> pdb=" O   GLY A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 305
      removed outlier: 3.735A  pdb=" N   ARG A 305 " --> pdb=" O   LYS A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 320
      removed outlier: 3.850A  pdb=" N   ARG A 311 " --> pdb=" O   SER A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 346
    Processing helix  chain 'A' and resid 356 through 369
      removed outlier: 4.249A  pdb=" N   TRP A 362 " --> pdb=" O   PRO A 358 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   TYR A 363 " --> pdb=" O   ALA A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 399
      removed outlier: 4.040A  pdb=" N   SER A 391 " --> pdb=" O   GLY A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 417
      removed outlier: 4.610A  pdb=" N   VAL A 404 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLN A 417 " --> pdb=" O   TYR A 413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 177
      removed outlier: 4.266A  pdb=" N   ARG B 170 " --> pdb=" O   THR B 166 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   ALA B 174 " --> pdb=" O   ARG B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 207
    Processing helix  chain 'B' and resid 227 through 249
    Processing helix  chain 'B' and resid 253 through 260
    Processing helix  chain 'B' and resid 260 through 282
      Proline residue:  B 272  - end of helix
      removed outlier: 3.759A  pdb=" N   ASN B 282 " --> pdb=" O   VAL B 278 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 296
      removed outlier: 4.138A  pdb=" N   VAL B 290 " --> pdb=" O   SER B 286 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   THR B 291 " --> pdb=" O   GLY B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 305
      removed outlier: 3.739A  pdb=" N   ARG B 305 " --> pdb=" O   LYS B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 320
      removed outlier: 3.830A  pdb=" N   ARG B 311 " --> pdb=" O   SER B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 320 through 346
    Processing helix  chain 'B' and resid 356 through 369
      removed outlier: 4.230A  pdb=" N   TRP B 362 " --> pdb=" O   PRO B 358 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   TYR B 363 " --> pdb=" O   ALA B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 399
      removed outlier: 4.020A  pdb=" N   SER B 391 " --> pdb=" O   GLY B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 417
      removed outlier: 4.666A  pdb=" N   VAL B 404 " --> pdb=" O   LEU B 400 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLN B 417 " --> pdb=" O   TYR B 413 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 166 through 177
      removed outlier: 4.315A  pdb=" N   ARG C 170 " --> pdb=" O   THR C 166 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   ALA C 174 " --> pdb=" O   ARG C 170 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 182 through 205
    Processing helix  chain 'C' and resid 227 through 249
      removed outlier: 3.784A  pdb=" N   CYS C 231 " --> pdb=" O   VAL C 227 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 253 through 260
      removed outlier: 3.619A  pdb=" N   ARG C 259 " --> pdb=" O   TYR C 255 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 260 through 282
      Proline residue:  C 272  - end of helix
      removed outlier: 3.816A  pdb=" N   ASN C 282 " --> pdb=" O   VAL C 278 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 288 through 296
    Processing helix  chain 'C' and resid 297 through 305
      removed outlier: 3.743A  pdb=" N   ARG C 305 " --> pdb=" O   LYS C 302 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 307 through 320
      removed outlier: 3.799A  pdb=" N   ARG C 311 " --> pdb=" O   SER C 307 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 320 through 346
    Processing helix  chain 'C' and resid 356 through 369
      removed outlier: 4.158A  pdb=" N   TRP C 362 " --> pdb=" O   PRO C 358 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   TYR C 363 " --> pdb=" O   ALA C 359 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 380 through 399
      removed outlier: 4.024A  pdb=" N   SER C 391 " --> pdb=" O   GLY C 387 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 400 through 417
      removed outlier: 4.594A  pdb=" N   VAL C 404 " --> pdb=" O   LEU C 400 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLN C 417 " --> pdb=" O   TYR C 413 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 166 through 177
      removed outlier: 4.275A  pdb=" N   ARG D 170 " --> pdb=" O   THR D 166 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   ALA D 174 " --> pdb=" O   ARG D 170 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 182 through 207
    Processing helix  chain 'D' and resid 227 through 249
    Processing helix  chain 'D' and resid 253 through 260
    Processing helix  chain 'D' and resid 260 through 282
      Proline residue:  D 272  - end of helix
      removed outlier: 3.768A  pdb=" N   ASN D 282 " --> pdb=" O   VAL D 278 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 286 through 296
      removed outlier: 4.129A  pdb=" N   VAL D 290 " --> pdb=" O   SER D 286 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   THR D 291 " --> pdb=" O   GLY D 287 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 297 through 305
      removed outlier: 3.565A  pdb=" N   PHE D 301 " --> pdb=" O   PHE D 298 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ARG D 305 " --> pdb=" O   LYS D 302 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 307 through 320
      removed outlier: 3.840A  pdb=" N   ARG D 311 " --> pdb=" O   SER D 307 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 320 through 346
    Processing helix  chain 'D' and resid 356 through 369
      removed outlier: 4.260A  pdb=" N   TRP D 362 " --> pdb=" O   PRO D 358 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   TYR D 363 " --> pdb=" O   ALA D 359 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 380 through 399
      removed outlier: 4.016A  pdb=" N   SER D 391 " --> pdb=" O   GLY D 387 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 400 through 417
      removed outlier: 4.618A  pdb=" N   VAL D 404 " --> pdb=" O   LEU D 400 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   GLN D 417 " --> pdb=" O   TYR D 413 " (cutoff:3.500A)

    567 hydrogen bonds defined for protein.
    1644 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: 1.05

  Time building geometry restraints manager: 0.82 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2351
        1.35 -     1.46: 2134
        1.46 -     1.58: 3423
        1.58 -     1.70: 0
        1.70 -     1.82: 92
  Bond restraints: 8000
  Sorted by residual:
  bond pdb=" C   LEU A 271 "
       pdb=" N   PRO A 272 "
    ideal  model  delta    sigma   weight residual
    1.334  1.364 -0.030 1.51e-02 4.39e+03 3.82e+00
  bond pdb=" C   LEU C 400 "
       pdb=" N   PRO C 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.340 -0.008 8.90e-03 1.26e+04 7.70e-01
  bond pdb=" C   LEU D 400 "
       pdb=" N   PRO D 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.340 -0.008 8.90e-03 1.26e+04 7.45e-01
  bond pdb=" C   LEU B 400 "
       pdb=" N   PRO B 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.340 -0.008 8.90e-03 1.26e+04 7.33e-01
  bond pdb=" C   LEU A 400 "
       pdb=" N   PRO A 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.340 -0.007 8.90e-03 1.26e+04 6.56e-01
  ... (remaining 7995 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 10690
        1.73 -     3.45: 141
        3.45 -     5.18: 29
        5.18 -     6.90: 0
        6.90 -     8.63: 4
  Bond angle restraints: 10864
  Sorted by residual:
  angle pdb=" N   VAL C 171 "
        pdb=" CA  VAL C 171 "
        pdb=" C   VAL C 171 "
      ideal   model   delta    sigma   weight residual
     113.39  108.45    4.94 1.47e+00 4.63e-01 1.13e+01
  angle pdb=" CB  MET D 262 "
        pdb=" CG  MET D 262 "
        pdb=" SD  MET D 262 "
      ideal   model   delta    sigma   weight residual
     112.70  121.33   -8.63 3.00e+00 1.11e-01 8.27e+00
  angle pdb=" CB  MET C 262 "
        pdb=" CG  MET C 262 "
        pdb=" SD  MET C 262 "
      ideal   model   delta    sigma   weight residual
     112.70  121.11   -8.41 3.00e+00 1.11e-01 7.86e+00
  angle pdb=" CB  MET B 262 "
        pdb=" CG  MET B 262 "
        pdb=" SD  MET B 262 "
      ideal   model   delta    sigma   weight residual
     112.70  121.02   -8.32 3.00e+00 1.11e-01 7.69e+00
  angle pdb=" CB  MET A 262 "
        pdb=" CG  MET A 262 "
        pdb=" SD  MET A 262 "
      ideal   model   delta    sigma   weight residual
     112.70  121.02   -8.32 3.00e+00 1.11e-01 7.69e+00
  ... (remaining 10859 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.05: 4150
       16.05 -    32.10: 412
       32.10 -    48.15: 94
       48.15 -    64.20: 9
       64.20 -    80.25: 7
  Dihedral angle restraints: 4672
    sinusoidal: 1760
      harmonic: 2912
  Sorted by residual:
  dihedral pdb=" CA  ALA B 226 "
           pdb=" C   ALA B 226 "
           pdb=" N   VAL B 227 "
           pdb=" CA  VAL B 227 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.90   25.10     0      5.00e+00 4.00e-02 2.52e+01
  dihedral pdb=" CA  ALA A 226 "
           pdb=" C   ALA A 226 "
           pdb=" N   VAL A 227 "
           pdb=" CA  VAL A 227 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.93   24.07     0      5.00e+00 4.00e-02 2.32e+01
  dihedral pdb=" CA  ALA D 226 "
           pdb=" C   ALA D 226 "
           pdb=" N   VAL D 227 "
           pdb=" CA  VAL D 227 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.75   23.25     0      5.00e+00 4.00e-02 2.16e+01
  ... (remaining 4669 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 749
       0.026 -    0.052: 321
       0.052 -    0.078: 167
       0.078 -    0.104: 43
       0.104 -    0.130: 12
  Chirality restraints: 1292
  Sorted by residual:
  chirality pdb=" CA  VAL D 227 "
            pdb=" N   VAL D 227 "
            pdb=" C   VAL D 227 "
            pdb=" CB  VAL D 227 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.22e-01
  chirality pdb=" CA  VAL A 227 "
            pdb=" N   VAL A 227 "
            pdb=" C   VAL A 227 "
            pdb=" CB  VAL A 227 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.09e-01
  chirality pdb=" CB  VAL A 297 "
            pdb=" CA  VAL A 297 "
            pdb=" CG1 VAL A 297 "
            pdb=" CG2 VAL A 297 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.51   -0.12 2.00e-01 2.50e+01 3.53e-01
  ... (remaining 1289 not shown)

  Planarity restraints: 1316
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 271 "    0.043 5.00e-02 4.00e+02   6.39e-02 6.53e+00
        pdb=" N   PRO B 272 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO B 272 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 272 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 271 "   -0.040 5.00e-02 4.00e+02   6.02e-02 5.80e+00
        pdb=" N   PRO D 272 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO D 272 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO D 272 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE D 240 "   -0.010 2.00e-02 2.50e+03   1.94e-02 3.77e+00
        pdb=" C   PHE D 240 "    0.034 2.00e-02 2.50e+03
        pdb=" O   PHE D 240 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   THR D 241 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1313 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1619
        2.77 -     3.30: 8082
        3.30 -     3.84: 12863
        3.84 -     4.37: 14658
        4.37 -     4.90: 25308
  Nonbonded interactions: 62530
  Sorted by model distance:
  nonbonded pdb=" O   MET D 238 "
            pdb=" OG1 THR D 241 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   MET B 238 "
            pdb=" OG1 THR B 241 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   MET A 238 "
            pdb=" OG1 THR A 241 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OE2 GLU C 205 "
            pdb=" NH2 ARG C 296 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" OG  SER C 181 "
            pdb=" N   THR C 182 "
     model   vdw
     2.289 3.120
  ... (remaining 62525 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'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.540
  Find NCS groups from input model:        0.120
  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:             0.010
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8000  Z= 0.104
  Angle     :  0.511   8.627  10864  Z= 0.274
  Chirality :  0.037   0.130   1292
  Planarity :  0.005   0.064   1316
  Dihedral  : 13.400  80.246   2792
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.12 (0.26), residues: 976
  helix:  0.79 (0.19), residues: 732
  sheet:  None (None), residues: 0
  loop : -2.76 (0.34), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 170 
 TYR   0.014   0.001   TYR D 188 
 PHE   0.006   0.001   PHE B 343 
 TRP   0.008   0.001   TRP B 362 
 HIS   0.001   0.000   HIS C 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00199 ( 8000)
  covalent geometry    : angle       0.51116 (10864)
  hydrogen bonds       : bond        0.19030 (  567)
  hydrogen bonds       : angle       6.54345 ( 1644)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  379 LYS cc_start: 0.8468 (mtmt) cc_final: 0.8114 (mttp)
REVERT: B  379 LYS cc_start: 0.8460 (mtmt) cc_final: 0.7860 (mttm)
REVERT: C  318 LYS cc_start: 0.8522 (ttpp) cc_final: 0.8229 (ttpp)
REVERT: C  333 MET cc_start: 0.8069 (ttm) cc_final: 0.7661 (ttt)
REVERT: C  379 LYS cc_start: 0.8608 (mtmt) cc_final: 0.8077 (mttm)
REVERT: D  318 LYS cc_start: 0.8583 (ttpp) cc_final: 0.8297 (ttpp)
REVERT: D  379 LYS cc_start: 0.8420 (mtmt) cc_final: 0.8057 (mttp)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.0899
  time to fit residues: 16.2874
Evaluate side-chains
  103 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.0770
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.5338

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.198585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.157787 restraints weight = 8024.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 2.65
r_work: 0.3155 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.1452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8000  Z= 0.131
  Angle     :  0.529   4.918  10864  Z= 0.286
  Chirality :  0.041   0.147   1292
  Planarity :  0.005   0.054   1316
  Dihedral  :  3.992  24.875   1088
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  9.51 %
    Favored  : 89.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.75 (0.27), residues: 976
  helix:  1.39 (0.19), residues: 752
  sheet:  None (None), residues: 0
  loop : -2.67 (0.36), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 293 
 TYR   0.014   0.001   TYR C 188 
 PHE   0.013   0.001   PHE C 289 
 TRP   0.010   0.001   TRP C 362 
 HIS   0.002   0.001   HIS B 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8000)
  covalent geometry    : angle       0.52929 (10864)
  hydrogen bonds       : bond        0.04512 (  567)
  hydrogen bonds       : angle       4.05125 ( 1644)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 114
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  238 MET cc_start: 0.6092 (mmt) cc_final: 0.5441 (ptm)
REVERT: A  353 LYS cc_start: 0.8903 (mttt) cc_final: 0.8695 (mttt)
REVERT: B  379 LYS cc_start: 0.8921 (mtmt) cc_final: 0.8503 (mttm)
REVERT: C  289 PHE cc_start: 0.8421 (t80) cc_final: 0.8174 (t80)
REVERT: C  318 LYS cc_start: 0.8801 (ttpp) cc_final: 0.8389 (ttpp)
REVERT: C  333 MET cc_start: 0.8750 (ttm) cc_final: 0.8530 (mtp)
REVERT: C  379 LYS cc_start: 0.8917 (mtmt) cc_final: 0.8440 (mttm)
REVERT: C  396 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7402 (tp)
REVERT: D  238 MET cc_start: 0.6107 (mmt) cc_final: 0.5439 (ptm)
REVERT: D  298 PHE cc_start: 0.7815 (m-10) cc_final: 0.7566 (m-10)
REVERT: D  318 LYS cc_start: 0.8750 (ttpp) cc_final: 0.8350 (ttpp)
REVERT: D  353 LYS cc_start: 0.8919 (mttt) cc_final: 0.8679 (mttt)
  outliers start: 8
  outliers final: 3
  residues processed: 119
  average time/residue: 0.0875
  time to fit residues: 13.9522
Evaluate side-chains
  109 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 105
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  347 LYS
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  396 LEU
Chi-restraints excluded: chain D residue  300 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 24 optimal weight:   20.0000
   chunk 40 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   chunk 79 optimal weight:    2.9990
   chunk 91 optimal weight:    0.6980
   chunk 13 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 11 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 76 optimal weight:    0.3980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 416 ASN
B 416 ASN
C 416 ASN
D 416 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.195134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.153837 restraints weight = 7910.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 2.27
r_work: 0.3070 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2932 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.1835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8000  Z= 0.147
  Angle     :  0.530   4.795  10864  Z= 0.285
  Chirality :  0.041   0.135   1292
  Planarity :  0.005   0.054   1316
  Dihedral  :  3.981  26.820   1088
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 11.74 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.27), residues: 976
  helix:  1.68 (0.19), residues: 748
  sheet:  None (None), residues: 0
  loop : -2.75 (0.35), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 293 
 TYR   0.017   0.001   TYR A 188 
 PHE   0.013   0.001   PHE C 289 
 TRP   0.008   0.001   TRP A 362 
 HIS   0.002   0.000   HIS C 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 8000)
  covalent geometry    : angle       0.53040 (10864)
  hydrogen bonds       : bond        0.04427 (  567)
  hydrogen bonds       : angle       3.84304 ( 1644)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 116
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  238 MET cc_start: 0.6225 (mmt) cc_final: 0.5525 (ptt)
REVERT: A  289 PHE cc_start: 0.8022 (t80) cc_final: 0.7737 (t80)
REVERT: A  379 LYS cc_start: 0.9041 (mtmt) cc_final: 0.8624 (mttp)
REVERT: A  396 LEU cc_start: 0.7756 (tt) cc_final: 0.7545 (tp)
REVERT: B  238 MET cc_start: 0.6388 (mmt) cc_final: 0.5579 (ptt)
REVERT: B  379 LYS cc_start: 0.8978 (mtmt) cc_final: 0.8619 (mttm)
REVERT: C  289 PHE cc_start: 0.8515 (t80) cc_final: 0.8191 (t80)
REVERT: C  318 LYS cc_start: 0.8784 (ttpp) cc_final: 0.8359 (ttpp)
REVERT: C  353 LYS cc_start: 0.9020 (mttt) cc_final: 0.8773 (mttt)
REVERT: D  238 MET cc_start: 0.6228 (mmt) cc_final: 0.5512 (ptt)
REVERT: D  318 LYS cc_start: 0.8726 (ttpp) cc_final: 0.8321 (ttpp)
REVERT: D  379 LYS cc_start: 0.9051 (mtmt) cc_final: 0.8633 (mttp)
  outliers start: 23
  outliers final: 16
  residues processed: 125
  average time/residue: 0.0962
  time to fit residues: 16.0091
Evaluate side-chains
  130 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  221 CYS
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  347 LYS
Chi-restraints excluded: chain B residue  205 GLU
Chi-restraints excluded: chain B residue  347 LYS
Chi-restraints excluded: chain C residue  207 VAL
Chi-restraints excluded: chain C residue  238 MET
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  300 ILE
Chi-restraints excluded: chain C residue  322 SER
Chi-restraints excluded: chain C residue  396 LEU
Chi-restraints excluded: chain D residue  205 GLU
Chi-restraints excluded: chain D residue  221 CYS
Chi-restraints excluded: chain D residue  300 ILE
Chi-restraints excluded: chain D residue  347 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 66 optimal weight:    0.5980
   chunk 48 optimal weight:   20.0000
   chunk 59 optimal weight:    8.9990
   chunk 42 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 93 optimal weight:    0.5980
   overall best weight:    0.7782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.195923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.155072 restraints weight = 8001.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 2.45
r_work: 0.3075 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2938 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8000  Z= 0.127
  Angle     :  0.496   4.644  10864  Z= 0.269
  Chirality :  0.040   0.137   1292
  Planarity :  0.005   0.053   1316
  Dihedral  :  3.961  26.864   1088
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 13.26 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.27), residues: 976
  helix:  1.77 (0.19), residues: 748
  sheet:  None (None), residues: 0
  loop : -2.78 (0.35), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 293 
 TYR   0.016   0.001   TYR A 188 
 PHE   0.012   0.001   PHE C 289 
 TRP   0.007   0.001   TRP B 362 
 HIS   0.001   0.000   HIS C 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 8000)
  covalent geometry    : angle       0.49625 (10864)
  hydrogen bonds       : bond        0.03971 (  567)
  hydrogen bonds       : angle       3.69947 ( 1644)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  238 MET cc_start: 0.6269 (mmt) cc_final: 0.5564 (ptt)
REVERT: A  353 LYS cc_start: 0.8972 (mttt) cc_final: 0.8721 (mttt)
REVERT: A  379 LYS cc_start: 0.8996 (mtmt) cc_final: 0.8612 (mttp)
REVERT: B  238 MET cc_start: 0.6396 (mmt) cc_final: 0.5599 (ptt)
REVERT: B  353 LYS cc_start: 0.8985 (mttt) cc_final: 0.8772 (mttt)
REVERT: C  289 PHE cc_start: 0.8488 (t80) cc_final: 0.8175 (t80)
REVERT: C  318 LYS cc_start: 0.8768 (ttpp) cc_final: 0.8356 (ttpp)
REVERT: D  238 MET cc_start: 0.6308 (mmt) cc_final: 0.5583 (ptt)
REVERT: D  318 LYS cc_start: 0.8748 (ttpp) cc_final: 0.8368 (ttpp)
REVERT: D  353 LYS cc_start: 0.8991 (mttt) cc_final: 0.8718 (mttt)
REVERT: D  379 LYS cc_start: 0.8988 (mtmt) cc_final: 0.8607 (mttp)
  outliers start: 16
  outliers final: 15
  residues processed: 129
  average time/residue: 0.0927
  time to fit residues: 15.9552
Evaluate side-chains
  138 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  221 CYS
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain B residue  221 CYS
Chi-restraints excluded: chain B residue  333 MET
Chi-restraints excluded: chain C residue  238 MET
Chi-restraints excluded: chain C residue  253 SER
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  300 ILE
Chi-restraints excluded: chain C residue  396 LEU
Chi-restraints excluded: chain D residue  205 GLU
Chi-restraints excluded: chain D residue  221 CYS
Chi-restraints excluded: chain D residue  300 ILE
Chi-restraints excluded: chain D residue  333 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 85 optimal weight:    0.1980
   chunk 31 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 24 optimal weight:   20.0000
   chunk 83 optimal weight:   10.0000
   chunk 1 optimal weight:   10.0000
   chunk 16 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.0388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.187206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.137377 restraints weight = 7914.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 1.57
r_work: 0.3132 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3000 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8000  Z= 0.147
  Angle     :  0.526   5.917  10864  Z= 0.281
  Chirality :  0.041   0.138   1292
  Planarity :  0.005   0.052   1316
  Dihedral  :  3.986  27.929   1088
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 14.44 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.27), residues: 976
  helix:  1.77 (0.19), residues: 748
  sheet:  None (None), residues: 0
  loop : -2.78 (0.34), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 293 
 TYR   0.018   0.001   TYR A 188 
 PHE   0.015   0.001   PHE A 289 
 TRP   0.006   0.001   TRP B 362 
 HIS   0.002   0.001   HIS C 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 8000)
  covalent geometry    : angle       0.52554 (10864)
  hydrogen bonds       : bond        0.04140 (  567)
  hydrogen bonds       : angle       3.69145 ( 1644)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  238 MET cc_start: 0.5998 (mmt) cc_final: 0.5297 (ptt)
REVERT: A  289 PHE cc_start: 0.7911 (t80) cc_final: 0.7653 (t80)
REVERT: A  379 LYS cc_start: 0.8972 (mtmt) cc_final: 0.8570 (mttp)
REVERT: B  238 MET cc_start: 0.6031 (mmt) cc_final: 0.5292 (ptt)
REVERT: C  231 CYS cc_start: 0.8545 (m) cc_final: 0.8224 (m)
REVERT: C  289 PHE cc_start: 0.8377 (t80) cc_final: 0.8060 (t80)
REVERT: C  318 LYS cc_start: 0.8484 (ttpp) cc_final: 0.8071 (ttpp)
REVERT: C  353 LYS cc_start: 0.8815 (mttt) cc_final: 0.8520 (mttt)
REVERT: D  238 MET cc_start: 0.6045 (mmt) cc_final: 0.5310 (ptt)
REVERT: D  318 LYS cc_start: 0.8484 (ttpp) cc_final: 0.8063 (ttpp)
REVERT: D  353 LYS cc_start: 0.8872 (mttt) cc_final: 0.8663 (mttt)
REVERT: D  379 LYS cc_start: 0.8967 (mtmt) cc_final: 0.8572 (mttp)
  outliers start: 18
  outliers final: 17
  residues processed: 128
  average time/residue: 0.0945
  time to fit residues: 16.1098
Evaluate side-chains
  131 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  221 CYS
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain B residue  221 CYS
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  333 MET
Chi-restraints excluded: chain C residue  207 VAL
Chi-restraints excluded: chain C residue  238 MET
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  300 ILE
Chi-restraints excluded: chain C residue  322 SER
Chi-restraints excluded: chain C residue  396 LEU
Chi-restraints excluded: chain D residue  205 GLU
Chi-restraints excluded: chain D residue  221 CYS
Chi-restraints excluded: chain D residue  300 ILE
Chi-restraints excluded: chain D residue  333 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 72 optimal weight:   20.0000
   overall best weight:    1.3384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.184938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.135849 restraints weight = 7896.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 1.57
r_work: 0.3096 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.2471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8000  Z= 0.169
  Angle     :  0.548   5.564  10864  Z= 0.293
  Chirality :  0.042   0.141   1292
  Planarity :  0.005   0.052   1316
  Dihedral  :  4.110  29.923   1088
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 15.02 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.27), residues: 976
  helix:  1.50 (0.19), residues: 776
  sheet:  None (None), residues: 0
  loop : -2.46 (0.37), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 293 
 TYR   0.021   0.001   TYR B 188 
 PHE   0.013   0.001   PHE A 289 
 TRP   0.006   0.001   TRP C 362 
 HIS   0.002   0.001   HIS C 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 8000)
  covalent geometry    : angle       0.54774 (10864)
  hydrogen bonds       : bond        0.04391 (  567)
  hydrogen bonds       : angle       3.71556 ( 1644)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 121
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  238 MET cc_start: 0.6058 (mmt) cc_final: 0.5559 (ptt)
REVERT: A  353 LYS cc_start: 0.8827 (mttt) cc_final: 0.8529 (mttt)
REVERT: B  353 LYS cc_start: 0.8848 (mttt) cc_final: 0.8558 (mttt)
REVERT: C  318 LYS cc_start: 0.8467 (ttpp) cc_final: 0.8066 (ttpp)
REVERT: D  238 MET cc_start: 0.6083 (mmt) cc_final: 0.5582 (ptm)
REVERT: D  318 LYS cc_start: 0.8460 (ttpp) cc_final: 0.8032 (ttpp)
  outliers start: 25
  outliers final: 25
  residues processed: 137
  average time/residue: 0.0843
  time to fit residues: 15.7411
Evaluate side-chains
  144 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 119
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  221 CYS
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  205 GLU
Chi-restraints excluded: chain B residue  221 CYS
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  333 MET
Chi-restraints excluded: chain B residue  347 LYS
Chi-restraints excluded: chain B residue  396 LEU
Chi-restraints excluded: chain C residue  207 VAL
Chi-restraints excluded: chain C residue  238 MET
Chi-restraints excluded: chain C residue  253 SER
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  300 ILE
Chi-restraints excluded: chain C residue  396 LEU
Chi-restraints excluded: chain D residue  197 VAL
Chi-restraints excluded: chain D residue  205 GLU
Chi-restraints excluded: chain D residue  221 CYS
Chi-restraints excluded: chain D residue  300 ILE
Chi-restraints excluded: chain D residue  333 MET
Chi-restraints excluded: chain D residue  396 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 21 optimal weight:    0.2980
   chunk 4 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 76 optimal weight:    0.0170
   chunk 31 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0010
   chunk 70 optimal weight:    0.6980
   chunk 81 optimal weight:    7.9990
   chunk 72 optimal weight:   20.0000
   overall best weight:    0.4024

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.188625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 135)---------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.124604 restraints weight = 7838.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 1.78
r_work: 0.3157 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.2513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8000  Z= 0.111
  Angle     :  0.488   5.838  10864  Z= 0.260
  Chirality :  0.039   0.140   1292
  Planarity :  0.004   0.052   1316
  Dihedral  :  3.953  26.993   1088
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 17.02 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.27), residues: 976
  helix:  1.96 (0.19), residues: 752
  sheet:  None (None), residues: 0
  loop : -2.76 (0.34), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 293 
 TYR   0.015   0.001   TYR C 188 
 PHE   0.008   0.001   PHE B 343 
 TRP   0.002   0.000   TRP C 362 
 HIS   0.001   0.000   HIS C 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 8000)
  covalent geometry    : angle       0.48819 (10864)
  hydrogen bonds       : bond        0.03648 (  567)
  hydrogen bonds       : angle       3.54164 ( 1644)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  231 CYS cc_start: 0.8394 (m) cc_final: 0.7940 (m)
REVERT: A  238 MET cc_start: 0.6169 (mmt) cc_final: 0.5414 (ptt)
REVERT: A  289 PHE cc_start: 0.7920 (t80) cc_final: 0.7661 (t80)
REVERT: A  353 LYS cc_start: 0.8772 (mttt) cc_final: 0.8452 (mttt)
REVERT: B  238 MET cc_start: 0.6162 (mmt) cc_final: 0.5372 (ptt)
REVERT: B  353 LYS cc_start: 0.8754 (mttt) cc_final: 0.8448 (mttt)
REVERT: C  231 CYS cc_start: 0.8426 (m) cc_final: 0.8121 (m)
REVERT: C  318 LYS cc_start: 0.8455 (ttpp) cc_final: 0.8088 (ttpp)
REVERT: C  353 LYS cc_start: 0.8614 (mttt) cc_final: 0.8352 (mttt)
REVERT: D  231 CYS cc_start: 0.8321 (m) cc_final: 0.7884 (m)
REVERT: D  238 MET cc_start: 0.6200 (mmt) cc_final: 0.5429 (ptt)
REVERT: D  318 LYS cc_start: 0.8439 (ttpp) cc_final: 0.8034 (ttpp)
  outliers start: 17
  outliers final: 13
  residues processed: 123
  average time/residue: 0.0967
  time to fit residues: 15.9363
Evaluate side-chains
  126 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  205 GLU
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain C residue  238 MET
Chi-restraints excluded: chain C residue  253 SER
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  300 ILE
Chi-restraints excluded: chain C residue  322 SER
Chi-restraints excluded: chain D residue  197 VAL
Chi-restraints excluded: chain D residue  300 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 75 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   chunk 2 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 87 optimal weight:    0.7980
   chunk 59 optimal weight:    0.2980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.197007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.130318 restraints weight = 7873.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 1.93
r_work: 0.3099 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.2565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8000  Z= 0.124
  Angle     :  0.498   5.620  10864  Z= 0.264
  Chirality :  0.040   0.140   1292
  Planarity :  0.004   0.051   1316
  Dihedral  :  3.911  27.054   1088
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 17.49 %
    Favored  : 80.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.53 (0.27), residues: 976
  helix:  2.06 (0.19), residues: 748
  sheet:  None (None), residues: 0
  loop : -2.75 (0.34), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 293 
 TYR   0.015   0.001   TYR B 188 
 PHE   0.008   0.001   PHE B 343 
 TRP   0.006   0.001   TRP B 362 
 HIS   0.001   0.000   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 8000)
  covalent geometry    : angle       0.49751 (10864)
  hydrogen bonds       : bond        0.03721 (  567)
  hydrogen bonds       : angle       3.54823 ( 1644)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  231 CYS cc_start: 0.8334 (m) cc_final: 0.7880 (m)
REVERT: A  238 MET cc_start: 0.6009 (mmt) cc_final: 0.5256 (ptt)
REVERT: A  353 LYS cc_start: 0.8572 (mttt) cc_final: 0.8365 (mttt)
REVERT: B  231 CYS cc_start: 0.8307 (m) cc_final: 0.7863 (m)
REVERT: B  238 MET cc_start: 0.5994 (mmt) cc_final: 0.5218 (ptt)
REVERT: B  353 LYS cc_start: 0.8570 (mttt) cc_final: 0.8367 (mttt)
REVERT: C  231 CYS cc_start: 0.8411 (m) cc_final: 0.8085 (m)
REVERT: C  318 LYS cc_start: 0.8294 (ttpp) cc_final: 0.7924 (ttpp)
REVERT: C  353 LYS cc_start: 0.8693 (mttt) cc_final: 0.8369 (mttt)
REVERT: D  231 CYS cc_start: 0.8249 (m) cc_final: 0.7816 (m)
REVERT: D  238 MET cc_start: 0.6053 (mmt) cc_final: 0.5280 (ptt)
REVERT: D  318 LYS cc_start: 0.8286 (ttpp) cc_final: 0.7895 (ttpp)
  outliers start: 14
  outliers final: 14
  residues processed: 126
  average time/residue: 0.0835
  time to fit residues: 14.4689
Evaluate side-chains
  131 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  221 CYS
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain C residue  238 MET
Chi-restraints excluded: chain C residue  253 SER
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  300 ILE
Chi-restraints excluded: chain D residue  197 VAL
Chi-restraints excluded: chain D residue  205 GLU
Chi-restraints excluded: chain D residue  221 CYS
Chi-restraints excluded: chain D residue  300 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 73 optimal weight:    7.9990
   chunk 18 optimal weight:    0.8980
   chunk 32 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   chunk 53 optimal weight:   10.0000
   chunk 95 optimal weight:    0.0770
   overall best weight:    0.7338

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.186901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.140624 restraints weight = 7871.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3602 rms_B_bonded: 1.55
r_work: 0.3248 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.2605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8000  Z= 0.125
  Angle     :  0.499   6.005  10864  Z= 0.264
  Chirality :  0.040   0.142   1292
  Planarity :  0.004   0.051   1316
  Dihedral  :  3.914  27.131   1088
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 17.25 %
    Favored  : 80.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.60 (0.27), residues: 976
  helix:  2.11 (0.19), residues: 748
  sheet:  None (None), residues: 0
  loop : -2.72 (0.34), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 293 
 TYR   0.015   0.001   TYR D 188 
 PHE   0.018   0.001   PHE C 289 
 TRP   0.007   0.001   TRP C 362 
 HIS   0.001   0.000   HIS C 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 8000)
  covalent geometry    : angle       0.49941 (10864)
  hydrogen bonds       : bond        0.03753 (  567)
  hydrogen bonds       : angle       3.53556 ( 1644)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  231 CYS cc_start: 0.8469 (m) cc_final: 0.8004 (m)
REVERT: A  238 MET cc_start: 0.6030 (mmt) cc_final: 0.5336 (ptt)
REVERT: A  353 LYS cc_start: 0.8813 (mttt) cc_final: 0.8560 (mttt)
REVERT: B  231 CYS cc_start: 0.8440 (m) cc_final: 0.7959 (m)
REVERT: B  238 MET cc_start: 0.6310 (mmt) cc_final: 0.5514 (ptt)
REVERT: B  353 LYS cc_start: 0.8783 (mttt) cc_final: 0.8545 (mttt)
REVERT: B  379 LYS cc_start: 0.8977 (mtmt) cc_final: 0.8562 (mttp)
REVERT: C  318 LYS cc_start: 0.8500 (ttpp) cc_final: 0.8116 (ttpp)
REVERT: D  231 CYS cc_start: 0.8399 (m) cc_final: 0.7943 (m)
REVERT: D  238 MET cc_start: 0.6094 (mmt) cc_final: 0.5370 (ptt)
REVERT: D  318 LYS cc_start: 0.8517 (ttpp) cc_final: 0.8098 (ttpp)
  outliers start: 19
  outliers final: 19
  residues processed: 131
  average time/residue: 0.0764
  time to fit residues: 13.8836
Evaluate side-chains
  134 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  221 CYS
Chi-restraints excluded: chain A residue  243 GLU
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  221 CYS
Chi-restraints excluded: chain B residue  243 GLU
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain C residue  238 MET
Chi-restraints excluded: chain C residue  253 SER
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  300 ILE
Chi-restraints excluded: chain C residue  322 SER
Chi-restraints excluded: chain C residue  396 LEU
Chi-restraints excluded: chain D residue  197 VAL
Chi-restraints excluded: chain D residue  205 GLU
Chi-restraints excluded: chain D residue  243 GLU
Chi-restraints excluded: chain D residue  300 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 52 optimal weight:    0.5980
   chunk 91 optimal weight:    0.6980
   chunk 95 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 39 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9990
   chunk 47 optimal weight:    0.3980
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.187685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.139091 restraints weight = 7869.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 1.61
r_work: 0.3245 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3116 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.2645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8000  Z= 0.123
  Angle     :  0.498   5.871  10864  Z= 0.263
  Chirality :  0.040   0.149   1292
  Planarity :  0.004   0.051   1316
  Dihedral  :  3.899  26.882   1088
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 16.78 %
    Favored  : 80.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.63 (0.27), residues: 976
  helix:  2.13 (0.19), residues: 748
  sheet:  None (None), residues: 0
  loop : -2.70 (0.34), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 293 
 TYR   0.015   0.001   TYR B 188 
 PHE   0.021   0.001   PHE C 289 
 TRP   0.006   0.001   TRP D 362 
 HIS   0.001   0.000   HIS D 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 8000)
  covalent geometry    : angle       0.49829 (10864)
  hydrogen bonds       : bond        0.03707 (  567)
  hydrogen bonds       : angle       3.53060 ( 1644)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  231 CYS cc_start: 0.8441 (m) cc_final: 0.7963 (m)
REVERT: A  238 MET cc_start: 0.5977 (mmt) cc_final: 0.5252 (ptt)
REVERT: B  231 CYS cc_start: 0.8421 (m) cc_final: 0.7949 (m)
REVERT: B  238 MET cc_start: 0.6208 (mmt) cc_final: 0.5417 (ptt)
REVERT: B  379 LYS cc_start: 0.8967 (mtmt) cc_final: 0.8547 (mttp)
REVERT: C  318 LYS cc_start: 0.8475 (ttpp) cc_final: 0.8077 (ttpp)
REVERT: C  379 LYS cc_start: 0.8963 (mtmt) cc_final: 0.8533 (mttp)
REVERT: D  231 CYS cc_start: 0.8365 (m) cc_final: 0.7910 (m)
REVERT: D  238 MET cc_start: 0.6036 (mmt) cc_final: 0.5280 (ptt)
REVERT: D  318 LYS cc_start: 0.8447 (ttpp) cc_final: 0.8024 (ttpp)
  outliers start: 20
  outliers final: 20
  residues processed: 131
  average time/residue: 0.0839
  time to fit residues: 15.1043
Evaluate side-chains
  133 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  221 CYS
Chi-restraints excluded: chain A residue  243 GLU
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  221 CYS
Chi-restraints excluded: chain B residue  243 GLU
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain C residue  238 MET
Chi-restraints excluded: chain C residue  253 SER
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  300 ILE
Chi-restraints excluded: chain C residue  322 SER
Chi-restraints excluded: chain C residue  396 LEU
Chi-restraints excluded: chain D residue  197 VAL
Chi-restraints excluded: chain D residue  205 GLU
Chi-restraints excluded: chain D residue  221 CYS
Chi-restraints excluded: chain D residue  243 GLU
Chi-restraints excluded: chain D residue  300 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.194435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.154039 restraints weight = 7775.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 1.38
r_work: 0.3244 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.2675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8000  Z= 0.132
  Angle     :  0.512   5.822  10864  Z= 0.271
  Chirality :  0.040   0.149   1292
  Planarity :  0.004   0.051   1316
  Dihedral  :  3.934  27.187   1088
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 17.49 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.59 (0.27), residues: 976
  helix:  1.90 (0.19), residues: 772
  sheet:  None (None), residues: 0
  loop : -2.40 (0.36), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 293 
 TYR   0.016   0.001   TYR B 188 
 PHE   0.010   0.001   PHE A 289 
 TRP   0.006   0.001   TRP C 362 
 HIS   0.001   0.000   HIS D 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8000)
  covalent geometry    : angle       0.51183 (10864)
  hydrogen bonds       : bond        0.03792 (  567)
  hydrogen bonds       : angle       3.54024 ( 1644)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2192.67 seconds
wall clock time: 38 minutes 4.42 seconds (2284.42 seconds total)