Starting phenix.real_space_refine
on Fri Feb 14 08:48:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6mgv_9112/02_2025/6mgv_9112.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6mgv_9112/02_2025/6mgv_9112.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6mgv_9112/02_2025/6mgv_9112.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6mgv_9112/02_2025/6mgv_9112.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6mgv_9112/02_2025/6mgv_9112.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6mgv_9112/02_2025/6mgv_9112.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.021
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      48      5.16       5
     C    6744      2.51       5
     N    1650      2.21       5
     O    1708      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10150
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5075
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 634, 5075
          Classifications: {'peptide': 634}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 34, 'TRANS': 599}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 88
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 39
  Restraints were copied for chains:
    B
  Time building chain proxies: 9.58, per 1000 atoms: 0.94
  Number of scatterers: 10150
  At special positions: 0
  Unit cell: (123.05, 129.95, 95.45, 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      48     16.00
     O    1708      8.00
     N    1650      7.00
     C    6744      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.75
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2432

  Finding SS restraints...
    Secondary structure from input PDB file:
      70 helices and 2 sheets defined
      76.9% alpha, 3.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 29
    Processing helix  chain 'A' and resid 30 through 33
      removed outlier: 6.322A  pdb=" N   PHE A  33 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 30 through 33'
    Processing helix  chain 'A' and resid 34 through 39
    Processing helix  chain 'A' and resid 74 through 80
      removed outlier: 3.557A  pdb=" N   LEU A  80 " --> pdb=" O   MET A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 92
    Processing helix  chain 'A' and resid 92 through 121
      removed outlier: 4.048A  pdb=" N   TYR A 102 " --> pdb=" O   TYR A  98 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   TRP A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      Proline residue:  A 111  - end of helix
    Processing helix  chain 'A' and resid 157 through 195
    Processing helix  chain 'A' and resid 198 through 201
    Processing helix  chain 'A' and resid 216 through 229
    Processing helix  chain 'A' and resid 242 through 269
    Processing helix  chain 'A' and resid 290 through 313
    Processing helix  chain 'A' and resid 314 through 317
      removed outlier: 6.347A  pdb=" N   LYS A 317 " --> pdb=" O   ASN A 314 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 314 through 317'
    Processing helix  chain 'A' and resid 329 through 337
    Processing helix  chain 'A' and resid 360 through 366
      removed outlier: 3.710A  pdb=" N   ILE A 366 " --> pdb=" O   ASN A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 369
      No H-bonds generated for 'chain 'A' and resid 367 through 369'
    Processing helix  chain 'A' and resid 370 through 388
    Processing helix  chain 'A' and resid 389 through 400
    Processing helix  chain 'A' and resid 422 through 438
      Proline residue:  A 430  - end of helix
    Processing helix  chain 'A' and resid 440 through 452
    Processing helix  chain 'A' and resid 456 through 476
    Processing helix  chain 'A' and resid 477 through 489
    Processing helix  chain 'A' and resid 504 through 512
      Proline residue:  A 510  - end of helix
    Processing helix  chain 'A' and resid 512 through 524
    Processing helix  chain 'A' and resid 524 through 532
    Processing helix  chain 'A' and resid 534 through 548
    Processing helix  chain 'A' and resid 554 through 559
    Processing helix  chain 'A' and resid 565 through 584
      Proline residue:  A 571  - end of helix
    Processing helix  chain 'A' and resid 587 through 589
      No H-bonds generated for 'chain 'A' and resid 587 through 589'
    Processing helix  chain 'A' and resid 590 through 612
    Processing helix  chain 'A' and resid 623 through 646
    Processing helix  chain 'A' and resid 654 through 659
    Processing helix  chain 'A' and resid 659 through 677
    Processing helix  chain 'A' and resid 677 through 682
    Processing helix  chain 'A' and resid 684 through 699
    Processing helix  chain 'A' and resid 703 through 710
      removed outlier: 4.027A  pdb=" N   ASN A 710 " --> pdb=" O   GLY A 706 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 29
    Processing helix  chain 'B' and resid 30 through 33
      removed outlier: 6.323A  pdb=" N   PHE B  33 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 30 through 33'
    Processing helix  chain 'B' and resid 34 through 39
    Processing helix  chain 'B' and resid 74 through 80
      removed outlier: 3.557A  pdb=" N   LEU B  80 " --> pdb=" O   MET B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 92
    Processing helix  chain 'B' and resid 92 through 121
      removed outlier: 4.048A  pdb=" N   TYR B 102 " --> pdb=" O   TYR B  98 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   TRP B 103 " --> pdb=" O   LEU B  99 " (cutoff:3.500A)
      Proline residue:  B 111  - end of helix
    Processing helix  chain 'B' and resid 157 through 195
    Processing helix  chain 'B' and resid 198 through 201
    Processing helix  chain 'B' and resid 216 through 229
    Processing helix  chain 'B' and resid 242 through 269
    Processing helix  chain 'B' and resid 290 through 313
    Processing helix  chain 'B' and resid 314 through 317
      removed outlier: 6.347A  pdb=" N   LYS B 317 " --> pdb=" O   ASN B 314 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 314 through 317'
    Processing helix  chain 'B' and resid 329 through 337
    Processing helix  chain 'B' and resid 360 through 366
      removed outlier: 3.711A  pdb=" N   ILE B 366 " --> pdb=" O   ASN B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 369
      No H-bonds generated for 'chain 'B' and resid 367 through 369'
    Processing helix  chain 'B' and resid 370 through 388
    Processing helix  chain 'B' and resid 389 through 400
    Processing helix  chain 'B' and resid 422 through 438
      Proline residue:  B 430  - end of helix
    Processing helix  chain 'B' and resid 440 through 452
    Processing helix  chain 'B' and resid 456 through 476
    Processing helix  chain 'B' and resid 477 through 489
    Processing helix  chain 'B' and resid 504 through 512
      Proline residue:  B 510  - end of helix
    Processing helix  chain 'B' and resid 512 through 524
    Processing helix  chain 'B' and resid 524 through 532
    Processing helix  chain 'B' and resid 534 through 548
    Processing helix  chain 'B' and resid 554 through 559
    Processing helix  chain 'B' and resid 565 through 584
      Proline residue:  B 571  - end of helix
    Processing helix  chain 'B' and resid 587 through 589
      No H-bonds generated for 'chain 'B' and resid 587 through 589'
    Processing helix  chain 'B' and resid 590 through 612
    Processing helix  chain 'B' and resid 623 through 646
    Processing helix  chain 'B' and resid 654 through 659
    Processing helix  chain 'B' and resid 659 through 677
    Processing helix  chain 'B' and resid 677 through 682
    Processing helix  chain 'B' and resid 684 through 699
    Processing helix  chain 'B' and resid 703 through 710
      removed outlier: 4.027A  pdb=" N   ASN B 710 " --> pdb=" O   GLY B 706 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 240
      removed outlier: 5.602A  pdb=" N   ALA A 322 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 233 through 240
      removed outlier: 5.602A  pdb=" N   ALA B 322 " --> pdb=" O   VAL B 239 " (cutoff:3.500A)

    695 hydrogen bonds defined for protein.
    2055 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: 3.17

  Time building geometry restraints manager: 3.20 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2294
        1.33 -     1.45: 2924
        1.45 -     1.58: 5128
        1.58 -     1.70: 6
        1.70 -     1.83: 88
  Bond restraints: 10440
  Sorted by residual:
  bond pdb=" N   PRO B 210 "
       pdb=" CD  PRO B 210 "
    ideal  model  delta    sigma   weight residual
    1.473  1.410  0.063 1.40e-02 5.10e+03 2.03e+01
  bond pdb=" N   PRO A 210 "
       pdb=" CD  PRO A 210 "
    ideal  model  delta    sigma   weight residual
    1.473  1.410  0.063 1.40e-02 5.10e+03 2.03e+01
  bond pdb=" CB  GLN B 615 "
       pdb=" CG  GLN B 615 "
    ideal  model  delta    sigma   weight residual
    1.520  1.407  0.113 3.00e-02 1.11e+03 1.43e+01
  bond pdb=" CB  GLN A 615 "
       pdb=" CG  GLN A 615 "
    ideal  model  delta    sigma   weight residual
    1.520  1.407  0.113 3.00e-02 1.11e+03 1.43e+01
  bond pdb=" N   PRO A 715 "
       pdb=" CD  PRO A 715 "
    ideal  model  delta    sigma   weight residual
    1.473  1.424  0.049 1.40e-02 5.10e+03 1.21e+01
  ... (remaining 10435 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 12698
        2.27 -     4.53: 1340
        4.53 -     6.80: 126
        6.80 -     9.06: 34
        9.06 -    11.33: 2
  Bond angle restraints: 14200
  Sorted by residual:
  angle pdb=" N   SER B 619 "
        pdb=" CA  SER B 619 "
        pdb=" C   SER B 619 "
      ideal   model   delta    sigma   weight residual
     110.17   98.84   11.33 1.61e+00 3.86e-01 4.95e+01
  angle pdb=" N   SER A 619 "
        pdb=" CA  SER A 619 "
        pdb=" C   SER A 619 "
      ideal   model   delta    sigma   weight residual
     110.17   98.86   11.31 1.61e+00 3.86e-01 4.94e+01
  angle pdb=" N   ASP A 554 "
        pdb=" CA  ASP A 554 "
        pdb=" C   ASP A 554 "
      ideal   model   delta    sigma   weight residual
     113.17  105.63    7.54 1.26e+00 6.30e-01 3.58e+01
  angle pdb=" N   ASP B 554 "
        pdb=" CA  ASP B 554 "
        pdb=" C   ASP B 554 "
      ideal   model   delta    sigma   weight residual
     113.17  105.68    7.49 1.26e+00 6.30e-01 3.54e+01
  angle pdb=" N   LYS A  41 "
        pdb=" CA  LYS A  41 "
        pdb=" C   LYS A  41 "
      ideal   model   delta    sigma   weight residual
     110.41  103.15    7.26 1.23e+00 6.61e-01 3.48e+01
  ... (remaining 14195 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.74: 5849
       14.74 -    29.49: 209
       29.49 -    44.23: 38
       44.23 -    58.98: 26
       58.98 -    73.72: 6
  Dihedral angle restraints: 6128
    sinusoidal: 2386
      harmonic: 3742
  Sorted by residual:
  dihedral pdb=" CA  ASP A 212 "
           pdb=" CB  ASP A 212 "
           pdb=" CG  ASP A 212 "
           pdb=" OD1 ASP A 212 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -82.32   52.32     1      2.00e+01 2.50e-03 9.33e+00
  dihedral pdb=" CA  ASP B 212 "
           pdb=" CB  ASP B 212 "
           pdb=" CG  ASP B 212 "
           pdb=" OD1 ASP B 212 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -82.29   52.29     1      2.00e+01 2.50e-03 9.32e+00
  dihedral pdb=" N   TYR A 613 "
           pdb=" C   TYR A 613 "
           pdb=" CA  TYR A 613 "
           pdb=" CB  TYR A 613 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  130.19   -7.39     0      2.50e+00 1.60e-01 8.74e+00
  ... (remaining 6125 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 1089
       0.075 -    0.150: 401
       0.150 -    0.225: 81
       0.225 -    0.300: 28
       0.300 -    0.375: 5
  Chirality restraints: 1604
  Sorted by residual:
  chirality pdb=" CA  PHE A 109 "
            pdb=" N   PHE A 109 "
            pdb=" C   PHE A 109 "
            pdb=" CB  PHE A 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.51e+00
  chirality pdb=" CA  PHE B 109 "
            pdb=" N   PHE B 109 "
            pdb=" C   PHE B 109 "
            pdb=" CB  PHE B 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.46e+00
  chirality pdb=" CA  TYR A 613 "
            pdb=" N   TYR A 613 "
            pdb=" C   TYR A 613 "
            pdb=" CB  TYR A 613 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.84e+00
  ... (remaining 1601 not shown)

  Planarity restraints: 1762
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 352 "   -0.041 2.00e-02 2.50e+03   1.98e-02 9.81e+00
        pdb=" CG  TRP B 352 "    0.014 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 352 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 352 "    0.021 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 352 "    0.008 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 352 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 352 "    0.024 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 352 "   -0.023 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 352 "    0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 352 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 519 "    0.036 2.00e-02 2.50e+03   2.20e-02 9.64e+00
        pdb=" CG  TYR A 519 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 519 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 519 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 519 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 519 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 519 "   -0.012 2.00e-02 2.50e+03
        pdb=" OH  TYR A 519 "    0.040 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 352 "    0.040 2.00e-02 2.50e+03   1.96e-02 9.62e+00
        pdb=" CG  TRP A 352 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 352 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 352 "   -0.021 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 352 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 352 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 352 "   -0.023 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 352 "    0.023 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 352 "   -0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 352 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1759 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 192
        2.65 -     3.21: 10310
        3.21 -     3.77: 16551
        3.77 -     4.34: 22521
        4.34 -     4.90: 36727
  Nonbonded interactions: 86301
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG B 330 "
            pdb=" OE1 GLU B 695 "
     model   vdw
     2.082 3.120
  nonbonded pdb=" NH2 ARG A 330 "
            pdb=" OE1 GLU A 695 "
     model   vdw
     2.082 3.120
  nonbonded pdb=" OH  TYR A 167 "
            pdb=" O   PHE A 657 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" OH  TYR B 167 "
            pdb=" O   PHE B 657 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" NH1 ARG A 330 "
            pdb=" OE1 GLU A 695 "
     model   vdw
     2.272 3.120
  ... (remaining 86296 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: 0.10
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=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:             0.350
  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:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     29.210
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
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      :  0.018   0.113  10440  Z= 1.176
  Angle     :  1.436  11.328  14200  Z= 0.968
  Chirality :  0.084   0.375   1604
  Planarity :  0.009   0.039   1762
  Dihedral  :  9.732  73.722   3696
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.37 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.22), residues: 1248
  helix:  0.35 (0.16), residues: 880
  sheet: -1.04 (0.73), residues: 46
  loop : -1.58 (0.32), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.006   TRP B 352 
 HIS   0.011   0.003   HIS B 293 
 PHE   0.045   0.008   PHE A  72 
 TYR   0.045   0.009   TYR A  38 
 ARG   0.007   0.001   ARG B 330 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 1.271 
Fit side-chains
REVERT: A  320 MET cc_start: 0.8368 (mmm) cc_final: 0.8164 (mmp)
REVERT: A  638 SER cc_start: 0.8300 (t) cc_final: 0.8039 (p)
REVERT: A  689 MET cc_start: 0.9055 (tpp) cc_final: 0.8805 (tpt)
REVERT: B  320 MET cc_start: 0.8363 (mmm) cc_final: 0.8159 (mmp)
REVERT: B  638 SER cc_start: 0.8302 (t) cc_final: 0.8039 (p)
REVERT: B  689 MET cc_start: 0.9053 (tpp) cc_final: 0.8814 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 229
  average time/residue: 0.2623
  time to fit residues: 79.9955
Evaluate side-chains
  163 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 1.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 98 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   chunk 73 optimal weight:    0.8980
   chunk 114 optimal weight:    0.7980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 340 GLN
A 341 GLN
A 363 ASN
A 607 HIS
A 608 GLN
A 614 ASN
B 340 GLN
B 341 GLN
B 363 ASN
B 607 HIS
B 608 GLN
B 614 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.161205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.130628 restraints weight = 11693.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 1.46
r_work: 0.3258 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3133 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.2638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10440  Z= 0.230
  Angle     :  0.632   6.709  14200  Z= 0.341
  Chirality :  0.044   0.178   1604
  Planarity :  0.005   0.046   1762
  Dihedral  :  4.667  21.706   1360
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  4.06 %
    Favored  : 95.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.23), residues: 1248
  helix:  1.90 (0.17), residues: 858
  sheet: -1.20 (0.77), residues: 42
  loop : -1.33 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 624 
 HIS   0.004   0.001   HIS B 232 
 PHE   0.026   0.002   PHE B 428 
 TYR   0.013   0.002   TYR B  38 
 ARG   0.007   0.001   ARG A 606 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 187
  time to evaluate  : 1.098 
Fit side-chains
REVERT: A  165 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.6295 (mtp)
REVERT: A  299 ASP cc_start: 0.7249 (t70) cc_final: 0.7045 (t0)
REVERT: A  320 MET cc_start: 0.8844 (mmm) cc_final: 0.8605 (mmp)
REVERT: A  437 PHE cc_start: 0.8068 (m-80) cc_final: 0.7755 (m-80)
REVERT: A  531 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.6939 (mt-10)
REVERT: A  559 MET cc_start: 0.7260 (ttp) cc_final: 0.6755 (ptm)
REVERT: A  638 SER cc_start: 0.8292 (t) cc_final: 0.7810 (p)
REVERT: A  689 MET cc_start: 0.9311 (tpp) cc_final: 0.9065 (tpt)
REVERT: B  165 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6287 (mtp)
REVERT: B  299 ASP cc_start: 0.7250 (t70) cc_final: 0.7046 (t0)
REVERT: B  320 MET cc_start: 0.8847 (mmm) cc_final: 0.8609 (mmp)
REVERT: B  437 PHE cc_start: 0.8080 (m-80) cc_final: 0.7743 (m-80)
REVERT: B  531 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6950 (mt-10)
REVERT: B  559 MET cc_start: 0.7263 (ttp) cc_final: 0.6755 (ptm)
REVERT: B  638 SER cc_start: 0.8279 (t) cc_final: 0.7796 (p)
REVERT: B  689 MET cc_start: 0.9313 (tpp) cc_final: 0.9069 (tpt)
  outliers start: 7
  outliers final: 0
  residues processed: 188
  average time/residue: 0.2027
  time to fit residues: 55.3758
Evaluate side-chains
  154 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 150
  time to evaluate  : 1.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 MET
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain B residue  165 MET
Chi-restraints excluded: chain B residue  531 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0370
   chunk 3 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 85 optimal weight:    0.0270
   chunk 22 optimal weight:    0.0050
   chunk 65 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.3530

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
B  31 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.162688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.132220 restraints weight = 11768.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 1.46
r_work: 0.3283 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10440  Z= 0.163
  Angle     :  0.553   6.563  14200  Z= 0.292
  Chirality :  0.041   0.139   1604
  Planarity :  0.004   0.054   1762
  Dihedral  :  4.435  23.310   1360
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  6.33 %
    Favored  : 93.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.24), residues: 1248
  helix:  2.15 (0.17), residues: 850
  sheet: -1.16 (0.78), residues: 46
  loop : -1.57 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 624 
 HIS   0.003   0.001   HIS B 379 
 PHE   0.024   0.002   PHE B 428 
 TYR   0.008   0.001   TYR A  43 
 ARG   0.005   0.001   ARG A 698 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 169
  time to evaluate  : 1.052 
Fit side-chains
REVERT: A  165 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6439 (mtp)
REVERT: A  320 MET cc_start: 0.8739 (mmm) cc_final: 0.8474 (mmp)
REVERT: A  390 ILE cc_start: 0.8305 (mm) cc_final: 0.7876 (mm)
REVERT: A  437 PHE cc_start: 0.8147 (m-80) cc_final: 0.7700 (m-80)
REVERT: A  531 GLU cc_start: 0.7270 (mp0) cc_final: 0.6487 (mm-30)
REVERT: A  559 MET cc_start: 0.7218 (ttp) cc_final: 0.6876 (ptm)
REVERT: A  638 SER cc_start: 0.8242 (t) cc_final: 0.7794 (p)
REVERT: A  645 LEU cc_start: 0.6159 (tt) cc_final: 0.5872 (tp)
REVERT: A  670 HIS cc_start: 0.8133 (m-70) cc_final: 0.7358 (t-170)
REVERT: A  689 MET cc_start: 0.9311 (tpp) cc_final: 0.9067 (tpt)
REVERT: B  165 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6430 (mtp)
REVERT: B  320 MET cc_start: 0.8732 (mmm) cc_final: 0.8468 (mmp)
REVERT: B  390 ILE cc_start: 0.8321 (mm) cc_final: 0.7898 (mm)
REVERT: B  437 PHE cc_start: 0.8121 (m-80) cc_final: 0.7658 (m-80)
REVERT: B  531 GLU cc_start: 0.7232 (mp0) cc_final: 0.6475 (mm-30)
REVERT: B  559 MET cc_start: 0.7222 (ttp) cc_final: 0.6876 (ptm)
REVERT: B  564 ILE cc_start: 0.8454 (tp) cc_final: 0.8207 (tp)
REVERT: B  638 SER cc_start: 0.8233 (t) cc_final: 0.7783 (p)
REVERT: B  645 LEU cc_start: 0.6159 (tt) cc_final: 0.5875 (tp)
REVERT: B  689 MET cc_start: 0.9312 (tpp) cc_final: 0.9073 (tpt)
  outliers start: 7
  outliers final: 1
  residues processed: 170
  average time/residue: 0.1917
  time to fit residues: 48.0265
Evaluate side-chains
  155 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 152
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 MET
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain B residue  165 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 118 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 42 optimal weight:    6.9990
   chunk 44 optimal weight:    5.9990
   chunk 92 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 47 optimal weight:    7.9990
   chunk 15 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 101 optimal weight:    0.7980
   chunk 21 optimal weight:    4.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 363 ASN
A 542 HIS
B 363 ASN
B 542 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.155660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.120872 restraints weight = 11852.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 1.37
r_work: 0.3171 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3048 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.3351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  10440  Z= 0.338
  Angle     :  0.615   6.238  14200  Z= 0.324
  Chirality :  0.045   0.154   1604
  Planarity :  0.005   0.055   1762
  Dihedral  :  4.610  25.015   1360
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  7.94 %
    Favored  : 90.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.24), residues: 1248
  helix:  2.05 (0.17), residues: 846
  sheet: -1.41 (0.73), residues: 46
  loop : -1.61 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 624 
 HIS   0.005   0.001   HIS B 714 
 PHE   0.023   0.002   PHE A 428 
 TYR   0.015   0.002   TYR A 181 
 ARG   0.007   0.001   ARG B 606 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 173
  time to evaluate  : 0.927 
Fit side-chains
REVERT: A  165 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6419 (mtp)
REVERT: A  247 ASP cc_start: 0.7965 (m-30) cc_final: 0.7762 (m-30)
REVERT: A  320 MET cc_start: 0.8860 (mmm) cc_final: 0.8620 (mmp)
REVERT: A  437 PHE cc_start: 0.8086 (m-80) cc_final: 0.7594 (m-80)
REVERT: A  531 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6710 (mt-10)
REVERT: A  559 MET cc_start: 0.7354 (ttp) cc_final: 0.6888 (ptm)
REVERT: A  638 SER cc_start: 0.8341 (t) cc_final: 0.7863 (p)
REVERT: A  645 LEU cc_start: 0.6172 (tt) cc_final: 0.5872 (tp)
REVERT: A  670 HIS cc_start: 0.8286 (m-70) cc_final: 0.7372 (t-170)
REVERT: A  689 MET cc_start: 0.9259 (tpp) cc_final: 0.9028 (tpt)
REVERT: B  165 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6394 (mtp)
REVERT: B  320 MET cc_start: 0.8859 (mmm) cc_final: 0.8618 (mmp)
REVERT: B  437 PHE cc_start: 0.8047 (m-80) cc_final: 0.7598 (m-80)
REVERT: B  531 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6721 (mt-10)
REVERT: B  559 MET cc_start: 0.7287 (ttp) cc_final: 0.6835 (ptm)
REVERT: B  638 SER cc_start: 0.8337 (t) cc_final: 0.7859 (p)
REVERT: B  645 LEU cc_start: 0.6185 (tt) cc_final: 0.5885 (tp)
REVERT: B  689 MET cc_start: 0.9263 (tpp) cc_final: 0.9033 (tpt)
  outliers start: 14
  outliers final: 7
  residues processed: 177
  average time/residue: 0.1856
  time to fit residues: 48.8590
Evaluate side-chains
  177 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 166
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue  165 MET
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  643 MET
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue  165 MET
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  643 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 34 optimal weight:   10.0000
   chunk 111 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 81 optimal weight:    0.0980
   chunk 15 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 93 optimal weight:    0.8980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A 363 ASN
B 363 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.160088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.125906 restraints weight = 11771.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 1.37
r_work: 0.3209 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3086 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.3700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10440  Z= 0.170
  Angle     :  0.522   6.016  14200  Z= 0.276
  Chirality :  0.041   0.142   1604
  Planarity :  0.005   0.055   1762
  Dihedral  :  4.306  23.734   1360
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  :  8.51 %
    Favored  : 89.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.24), residues: 1248
  helix:  2.28 (0.18), residues: 836
  sheet: -1.59 (0.74), residues: 46
  loop : -1.46 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 624 
 HIS   0.003   0.001   HIS B 379 
 PHE   0.025   0.001   PHE A 428 
 TYR   0.006   0.001   TYR A 233 
 ARG   0.004   0.000   ARG B 606 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 174
  time to evaluate  : 1.049 
Fit side-chains
REVERT: A  165 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6461 (mtp)
REVERT: A  320 MET cc_start: 0.8791 (mmm) cc_final: 0.8481 (mmp)
REVERT: A  388 PHE cc_start: 0.7337 (m-10) cc_final: 0.7102 (m-10)
REVERT: A  531 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6326 (mm-30)
REVERT: A  559 MET cc_start: 0.7208 (ttp) cc_final: 0.6702 (ptm)
REVERT: A  638 SER cc_start: 0.8282 (t) cc_final: 0.7795 (p)
REVERT: A  670 HIS cc_start: 0.8204 (m-70) cc_final: 0.7265 (t-170)
REVERT: A  689 MET cc_start: 0.9287 (tpp) cc_final: 0.9059 (tpt)
REVERT: B  165 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6463 (mtp)
REVERT: B  320 MET cc_start: 0.8786 (mmm) cc_final: 0.8479 (mmp)
REVERT: B  531 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6338 (mm-30)
REVERT: B  559 MET cc_start: 0.7207 (ttp) cc_final: 0.6693 (ptm)
REVERT: B  638 SER cc_start: 0.8273 (t) cc_final: 0.7785 (p)
REVERT: B  689 MET cc_start: 0.9292 (tpp) cc_final: 0.9065 (tpt)
  outliers start: 16
  outliers final: 6
  residues processed: 179
  average time/residue: 0.1820
  time to fit residues: 48.4807
Evaluate side-chains
  179 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 169
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 MET
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  643 MET
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue  165 MET
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  643 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 17 optimal weight:    4.9990
   chunk 83 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 111 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9980
   chunk 91 optimal weight:    0.5980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** 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 = 0.3784 r_free = 0.3784 target = 0.158977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.124787 restraints weight = 11809.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 1.36
r_work: 0.3195 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.3795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10440  Z= 0.184
  Angle     :  0.535   7.712  14200  Z= 0.278
  Chirality :  0.041   0.179   1604
  Planarity :  0.005   0.056   1762
  Dihedral  :  4.240  24.207   1360
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  8.70 %
    Favored  : 89.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.24), residues: 1248
  helix:  2.35 (0.18), residues: 836
  sheet: -1.70 (0.73), residues: 46
  loop : -1.52 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 624 
 HIS   0.004   0.001   HIS A 542 
 PHE   0.026   0.002   PHE B 428 
 TYR   0.006   0.001   TYR B 469 
 ARG   0.003   0.000   ARG B 606 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 175
  time to evaluate  : 1.122 
Fit side-chains
REVERT: A  165 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6494 (mtp)
REVERT: A  320 MET cc_start: 0.8803 (mmm) cc_final: 0.8490 (mmp)
REVERT: A  388 PHE cc_start: 0.7349 (m-10) cc_final: 0.7119 (m-10)
REVERT: A  531 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6337 (mm-30)
REVERT: A  559 MET cc_start: 0.7241 (ttp) cc_final: 0.6786 (ptm)
REVERT: A  638 SER cc_start: 0.8281 (t) cc_final: 0.7777 (p)
REVERT: A  670 HIS cc_start: 0.8240 (m-70) cc_final: 0.7297 (t-170)
REVERT: A  689 MET cc_start: 0.9279 (tpp) cc_final: 0.9041 (tpt)
REVERT: B  165 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6486 (mtp)
REVERT: B  320 MET cc_start: 0.8800 (mmm) cc_final: 0.8493 (mmp)
REVERT: B  480 SER cc_start: 0.8182 (m) cc_final: 0.7932 (p)
REVERT: B  531 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6351 (mm-30)
REVERT: B  559 MET cc_start: 0.7230 (ttp) cc_final: 0.6772 (ptm)
REVERT: B  638 SER cc_start: 0.8275 (t) cc_final: 0.7774 (p)
REVERT: B  689 MET cc_start: 0.9279 (tpp) cc_final: 0.9044 (tpt)
  outliers start: 14
  outliers final: 7
  residues processed: 176
  average time/residue: 0.1947
  time to fit residues: 50.7291
Evaluate side-chains
  181 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 170
  time to evaluate  : 1.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 MET
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  643 MET
Chi-restraints excluded: chain B residue  165 MET
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  470 ILE
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  643 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 123 optimal weight:    0.8980
   chunk 120 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 3 optimal weight:    0.1980
   chunk 114 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 363 ASN
B 542 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.159645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.125415 restraints weight = 11910.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 1.38
r_work: 0.3193 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3075 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.3967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10440  Z= 0.173
  Angle     :  0.526   6.751  14200  Z= 0.273
  Chirality :  0.041   0.196   1604
  Planarity :  0.005   0.056   1762
  Dihedral  :  4.148  23.212   1360
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  8.70 %
    Favored  : 89.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.24), residues: 1248
  helix:  2.38 (0.17), residues: 836
  sheet: -1.72 (0.74), residues: 46
  loop : -1.55 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 624 
 HIS   0.004   0.001   HIS B 542 
 PHE   0.026   0.002   PHE B 428 
 TYR   0.006   0.001   TYR A 583 
 ARG   0.002   0.000   ARG A 698 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 178
  time to evaluate  : 1.189 
Fit side-chains
REVERT: A  165 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6543 (mtp)
REVERT: A  320 MET cc_start: 0.8794 (mmm) cc_final: 0.8479 (mmp)
REVERT: A  395 PHE cc_start: 0.6861 (m-10) cc_final: 0.6397 (m-10)
REVERT: A  437 PHE cc_start: 0.8244 (m-80) cc_final: 0.7875 (m-80)
REVERT: A  531 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6296 (mm-30)
REVERT: A  559 MET cc_start: 0.7248 (ttp) cc_final: 0.6812 (ptm)
REVERT: A  638 SER cc_start: 0.8240 (t) cc_final: 0.7726 (p)
REVERT: A  643 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6788 (ttm)
REVERT: A  670 HIS cc_start: 0.8241 (m-70) cc_final: 0.7307 (t-170)
REVERT: B  165 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6541 (mtp)
REVERT: B  320 MET cc_start: 0.8797 (mmm) cc_final: 0.8488 (mmp)
REVERT: B  437 PHE cc_start: 0.8249 (m-80) cc_final: 0.7878 (m-80)
REVERT: B  531 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6324 (mm-30)
REVERT: B  559 MET cc_start: 0.7248 (ttp) cc_final: 0.6810 (ptm)
REVERT: B  638 SER cc_start: 0.8229 (t) cc_final: 0.7715 (p)
REVERT: B  643 MET cc_start: 0.7043 (OUTLIER) cc_final: 0.6799 (ttm)
  outliers start: 15
  outliers final: 7
  residues processed: 178
  average time/residue: 0.1939
  time to fit residues: 50.5289
Evaluate side-chains
  186 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 173
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 MET
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  643 MET
Chi-restraints excluded: chain B residue  165 MET
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  470 ILE
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  643 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 86 optimal weight:    0.0870
   chunk 85 optimal weight:    0.0000
   chunk 62 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 82 optimal weight:    3.9990
   chunk 92 optimal weight:    4.9990
   chunk 68 optimal weight:    4.9990
   chunk 115 optimal weight:    0.9990
   chunk 120 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.4162

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 363 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.161045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.126976 restraints weight = 11923.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 1.38
r_work: 0.3238 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3117 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.4127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  10440  Z= 0.147
  Angle     :  0.516   8.054  14200  Z= 0.266
  Chirality :  0.041   0.249   1604
  Planarity :  0.004   0.055   1762
  Dihedral  :  4.026  22.624   1360
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  :  9.26 %
    Favored  : 89.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.24), residues: 1248
  helix:  2.44 (0.17), residues: 836
  sheet: -1.72 (0.76), residues: 46
  loop : -1.54 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 624 
 HIS   0.007   0.001   HIS B 542 
 PHE   0.028   0.001   PHE B 428 
 TYR   0.005   0.001   TYR B 469 
 ARG   0.003   0.000   ARG B 698 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 185
  time to evaluate  : 1.081 
Fit side-chains
REVERT: A  165 MET cc_start: 0.7028 (OUTLIER) cc_final: 0.6549 (mtp)
REVERT: A  320 MET cc_start: 0.8795 (mmm) cc_final: 0.8490 (mmp)
REVERT: A  437 PHE cc_start: 0.8230 (m-80) cc_final: 0.7811 (m-80)
REVERT: A  531 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6332 (mm-30)
REVERT: A  559 MET cc_start: 0.7163 (ttp) cc_final: 0.6749 (ptm)
REVERT: A  638 SER cc_start: 0.8192 (t) cc_final: 0.7668 (p)
REVERT: A  643 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6869 (ttm)
REVERT: A  670 HIS cc_start: 0.8225 (m-70) cc_final: 0.7393 (t-170)
REVERT: B  165 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.6523 (mtp)
REVERT: B  320 MET cc_start: 0.8796 (mmm) cc_final: 0.8492 (mmp)
REVERT: B  395 PHE cc_start: 0.7026 (m-10) cc_final: 0.6552 (m-10)
REVERT: B  437 PHE cc_start: 0.8278 (m-80) cc_final: 0.7885 (m-80)
REVERT: B  531 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6350 (mm-30)
REVERT: B  559 MET cc_start: 0.7158 (ttp) cc_final: 0.6748 (ptm)
REVERT: B  638 SER cc_start: 0.8181 (t) cc_final: 0.7655 (p)
REVERT: B  643 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6877 (ttm)
  outliers start: 16
  outliers final: 8
  residues processed: 186
  average time/residue: 0.2116
  time to fit residues: 56.8148
Evaluate side-chains
  191 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 177
  time to evaluate  : 1.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 MET
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  388 PHE
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  643 MET
Chi-restraints excluded: chain B residue  165 MET
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  470 ILE
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  643 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 116 optimal weight:    4.9990
   chunk 113 optimal weight:    0.0970
   chunk 2 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 77 optimal weight:    0.7980
   chunk 44 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   chunk 35 optimal weight:    5.9990
   chunk 86 optimal weight:   10.0000
   chunk 46 optimal weight:    6.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 363 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.160004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.126124 restraints weight = 11875.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 1.37
r_work: 0.3213 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.4199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10440  Z= 0.170
  Angle     :  0.531  10.736  14200  Z= 0.271
  Chirality :  0.042   0.344   1604
  Planarity :  0.005   0.055   1762
  Dihedral  :  4.044  22.275   1360
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  9.17 %
    Favored  : 89.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.24), residues: 1248
  helix:  2.42 (0.17), residues: 836
  sheet: -1.76 (0.74), residues: 46
  loop : -1.57 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 624 
 HIS   0.003   0.001   HIS A 162 
 PHE   0.027   0.002   PHE B 428 
 TYR   0.005   0.001   TYR A 469 
 ARG   0.002   0.000   ARG A 698 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 183
  time to evaluate  : 1.167 
Fit side-chains
REVERT: A   76 MET cc_start: 0.8588 (mtt) cc_final: 0.8119 (mtt)
REVERT: A  165 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.6469 (mtp)
REVERT: A  320 MET cc_start: 0.8815 (mmm) cc_final: 0.8532 (mmp)
REVERT: A  395 PHE cc_start: 0.6706 (m-10) cc_final: 0.6316 (m-10)
REVERT: A  437 PHE cc_start: 0.8228 (m-80) cc_final: 0.7836 (m-80)
REVERT: A  531 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6198 (mm-30)
REVERT: A  559 MET cc_start: 0.7021 (ttp) cc_final: 0.6692 (ptm)
REVERT: A  638 SER cc_start: 0.8162 (t) cc_final: 0.7621 (p)
REVERT: A  643 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6879 (ttm)
REVERT: B   47 LEU cc_start: 0.8418 (mp) cc_final: 0.8216 (mt)
REVERT: B   76 MET cc_start: 0.8609 (mtt) cc_final: 0.8153 (mtt)
REVERT: B  165 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6452 (mtp)
REVERT: B  320 MET cc_start: 0.8807 (mmm) cc_final: 0.8524 (mmp)
REVERT: B  395 PHE cc_start: 0.6897 (m-10) cc_final: 0.6414 (m-10)
REVERT: B  437 PHE cc_start: 0.8198 (m-80) cc_final: 0.7840 (m-80)
REVERT: B  531 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6290 (mm-30)
REVERT: B  559 MET cc_start: 0.7020 (ttp) cc_final: 0.6691 (ptm)
REVERT: B  638 SER cc_start: 0.8141 (t) cc_final: 0.7599 (p)
REVERT: B  643 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6877 (ttm)
  outliers start: 14
  outliers final: 8
  residues processed: 183
  average time/residue: 0.2023
  time to fit residues: 54.1383
Evaluate side-chains
  196 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 182
  time to evaluate  : 1.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 MET
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  589 MET
Chi-restraints excluded: chain A residue  643 MET
Chi-restraints excluded: chain B residue  165 MET
Chi-restraints excluded: chain B residue  388 PHE
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  470 ILE
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  589 MET
Chi-restraints excluded: chain B residue  643 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 108 optimal weight:    0.7980
   chunk 110 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 44 optimal weight:    7.9990
   chunk 111 optimal weight:    0.9980
   chunk 88 optimal weight:    0.4980
   chunk 52 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 363 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.159418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.125512 restraints weight = 11861.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 1.37
r_work: 0.3204 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.4235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10440  Z= 0.175
  Angle     :  0.542  11.029  14200  Z= 0.274
  Chirality :  0.042   0.310   1604
  Planarity :  0.005   0.054   1762
  Dihedral  :  4.040  21.719   1360
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  9.74 %
    Favored  : 89.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.24), residues: 1248
  helix:  2.40 (0.17), residues: 836
  sheet: -1.76 (0.74), residues: 46
  loop : -1.58 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 624 
 HIS   0.007   0.001   HIS B 542 
 PHE   0.029   0.002   PHE A 382 
 TYR   0.005   0.001   TYR A 469 
 ARG   0.003   0.000   ARG B  48 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 182
  time to evaluate  : 1.048 
Fit side-chains
REVERT: A   76 MET cc_start: 0.8452 (mtt) cc_final: 0.7984 (mtt)
REVERT: A  165 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.6512 (mtp)
REVERT: A  320 MET cc_start: 0.8818 (mmm) cc_final: 0.8533 (mmp)
REVERT: A  395 PHE cc_start: 0.6883 (m-10) cc_final: 0.6449 (m-10)
REVERT: A  437 PHE cc_start: 0.8215 (m-80) cc_final: 0.7866 (m-80)
REVERT: A  531 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6216 (mm-30)
REVERT: A  559 MET cc_start: 0.6974 (ttp) cc_final: 0.6495 (ptm)
REVERT: A  638 SER cc_start: 0.8160 (t) cc_final: 0.7611 (p)
REVERT: A  643 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.7001 (ttm)
REVERT: B   76 MET cc_start: 0.8501 (mtt) cc_final: 0.8030 (mtt)
REVERT: B  165 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.6478 (mtp)
REVERT: B  320 MET cc_start: 0.8818 (mmm) cc_final: 0.8534 (mmp)
REVERT: B  395 PHE cc_start: 0.6891 (m-10) cc_final: 0.6401 (m-10)
REVERT: B  437 PHE cc_start: 0.8219 (m-80) cc_final: 0.7876 (m-80)
REVERT: B  531 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6312 (mm-30)
REVERT: B  559 MET cc_start: 0.6960 (ttp) cc_final: 0.6488 (ptm)
REVERT: B  638 SER cc_start: 0.8145 (t) cc_final: 0.7595 (p)
REVERT: B  643 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.7004 (ttm)
  outliers start: 13
  outliers final: 7
  residues processed: 182
  average time/residue: 0.1958
  time to fit residues: 52.4588
Evaluate side-chains
  191 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 178
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 MET
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  388 PHE
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  643 MET
Chi-restraints excluded: chain B residue  165 MET
Chi-restraints excluded: chain B residue  388 PHE
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  470 ILE
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  643 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 80 optimal weight:    0.0040
   chunk 34 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 109 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 75 optimal weight:    0.5980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.5992

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 363 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.160361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.130211 restraints weight = 11836.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 1.43
r_work: 0.3221 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3104 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.4327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  10440  Z= 0.155
  Angle     :  0.527  11.253  14200  Z= 0.268
  Chirality :  0.042   0.317   1604
  Planarity :  0.005   0.055   1762
  Dihedral  :  4.003  21.024   1360
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  9.74 %
    Favored  : 88.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.24), residues: 1248
  helix:  2.32 (0.17), residues: 860
  sheet: -1.72 (0.75), residues: 46
  loop : -1.88 (0.31), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 624 
 HIS   0.005   0.001   HIS B 162 
 PHE   0.034   0.002   PHE B 382 
 TYR   0.006   0.001   TYR B 469 
 ARG   0.003   0.000   ARG B  48 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5681.32 seconds
wall clock time: 101 minutes 17.05 seconds (6077.05 seconds total)