Starting phenix.real_space_refine
on Fri Aug 22 15:28:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ke9_37150/08_2025/8ke9_37150_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ke9_37150/08_2025/8ke9_37150.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ke9_37150/08_2025/8ke9_37150_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ke9_37150/08_2025/8ke9_37150_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ke9_37150/08_2025/8ke9_37150.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ke9_37150/08_2025/8ke9_37150.map"
  }
  resolution = 3.76
  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=   0.000 sd=   0.001
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: 3
    Type Number    sf(0)   Gaussians
     C    3105      2.51       5
     N     837      2.21       5
     O     987      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4929
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1643
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 211}
    Chain: "B"
      Number of atoms: 1643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1643
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 211}
    Chain: "C"
      Number of atoms: 1643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1643
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 211}
  Time building chain proxies: 1.61, per 1000 atoms: 0.33
  Number of scatterers: 4929
  At special positions: 0
  Unit cell: (66.34, 142.31, 100.58, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     987      8.00
     N     837      7.00
     C    3105      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: 0.46
  Conformation dependent library (CDL) restraints added in 204.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1170

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 11 sheets defined
      20.3% alpha, 36.1% 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 245 through 266
      removed outlier: 3.789A  pdb=" N   VAL A 249 " --> pdb=" O   ASP A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 280
    Processing helix  chain 'A' and resid 307 through 318
    Processing helix  chain 'B' and resid 247 through 266
    Processing helix  chain 'B' and resid 269 through 279
    Processing helix  chain 'B' and resid 307 through 317
    Processing helix  chain 'C' and resid 246 through 267
    Processing helix  chain 'C' and resid 269 through 280
    Processing helix  chain 'C' and resid 307 through 317
    Processing sheet with id=AA1, first strand: chain 'A' and resid 328 through 330
      removed outlier: 4.096A  pdb=" N   VAL A 454 " --> pdb=" O   THR A 374 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   THR A 374 " --> pdb=" O   VAL A 454 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   PHE A 456 " --> pdb=" O   THR A 372 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   THR A 372 " --> pdb=" O   PHE A 456 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   GLY A 458 " --> pdb=" O   LEU A 370 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   LEU A 370 " --> pdb=" O   GLY A 458 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 345 through 348
      removed outlier: 3.525A  pdb=" N   PHE A 321 " --> pdb=" O   GLY A 458 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   GLY A 458 " --> pdb=" O   PHE A 321 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   VAL A 454 " --> pdb=" O   THR A 374 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   THR A 374 " --> pdb=" O   VAL A 454 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   PHE A 456 " --> pdb=" O   THR A 372 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   THR A 372 " --> pdb=" O   PHE A 456 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   GLY A 458 " --> pdb=" O   LEU A 370 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   LEU A 370 " --> pdb=" O   GLY A 458 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLY A 423 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 339 through 340
      removed outlier: 6.717A  pdb=" N   VAL A 394 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   PHE A 404 " --> pdb=" O   VAL A 394 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 355 through 357
    Processing sheet with id=AA5, first strand: chain 'B' and resid 328 through 330
      removed outlier: 3.521A  pdb=" N   GLY B 458 " --> pdb=" O   PHE B 321 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   PHE B 321 " --> pdb=" O   GLY B 458 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 328 through 330
      removed outlier: 4.861A  pdb=" N   VAL B 449 " --> pdb=" O   VAL B 380 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   VAL B 380 " --> pdb=" O   VAL B 449 " (cutoff:3.500A)
      removed outlier: 5.347A  pdb=" N   LEU B 451 " --> pdb=" O   ALA B 378 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   ALA B 378 " --> pdb=" O   LEU B 451 " (cutoff:3.500A)
      removed outlier: 5.415A  pdb=" N   ASP B 453 " --> pdb=" O   ARG B 376 " (cutoff:3.500A)
      removed outlier: 4.877A  pdb=" N   ARG B 376 " --> pdb=" O   ASP B 453 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 339 through 340
      removed outlier: 3.579A  pdb=" N   ASN B 436 " --> pdb=" O   PHE B 393 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   ALA B 390 " --> pdb=" O   ARG B 407 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   ARG B 407 " --> pdb=" O   ALA B 390 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   LEU B 392 " --> pdb=" O   LEU B 405 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 355 through 357
      removed outlier: 3.627A  pdb=" N   ASN B 355 " --> pdb=" O   LEU B 362 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 345 through 348
      removed outlier: 4.177A  pdb=" N   PHE C 321 " --> pdb=" O   GLY C 458 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   VAL C 454 " --> pdb=" O   ARG C 325 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   GLY C 327 " --> pdb=" O   GLU C 452 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   GLU C 452 " --> pdb=" O   GLY C 327 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   GLN C 329 " --> pdb=" O   VAL C 450 " (cutoff:3.500A)
      removed outlier: 5.094A  pdb=" N   VAL C 450 " --> pdb=" O   GLN C 329 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   SER C 448 " --> pdb=" O   VAL C 380 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   VAL C 380 " --> pdb=" O   SER C 448 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   VAL C 454 " --> pdb=" O   THR C 374 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   THR C 374 " --> pdb=" O   VAL C 454 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   PHE C 456 " --> pdb=" O   THR C 372 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   THR C 372 " --> pdb=" O   PHE C 456 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   GLY C 458 " --> pdb=" O   LEU C 370 " (cutoff:3.500A)
      removed outlier: 6.117A  pdb=" N   LEU C 370 " --> pdb=" O   GLY C 458 " (cutoff:3.500A)
      removed outlier: 5.085A  pdb=" N   GLN C 460 " --> pdb=" O   THR C 368 " (cutoff:3.500A)
      removed outlier: 7.429A  pdb=" N   THR C 368 " --> pdb=" O   GLN C 460 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 339 through 340
      removed outlier: 3.755A  pdb=" N   ASN C 436 " --> pdb=" O   PHE C 393 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   PHE C 393 " --> pdb=" O   ASN C 436 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLN C 438 " --> pdb=" O   LEU C 391 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   ALA C 390 " --> pdb=" O   ARG C 407 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   ARG C 407 " --> pdb=" O   ALA C 390 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   LEU C 392 " --> pdb=" O   LEU C 405 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 355 through 356
      removed outlier: 3.604A  pdb=" N   ASN C 355 " --> pdb=" O   LEU C 362 " (cutoff:3.500A)

    227 hydrogen bonds defined for protein.
    609 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: 0.72

  Time building geometry restraints manager: 0.61 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 813
        1.29 -     1.35: 825
        1.35 -     1.42: 597
        1.42 -     1.49: 799
        1.49 -     1.56: 2000
  Bond restraints: 5034
  Sorted by residual:
  bond pdb=" C   VAL B 273 "
       pdb=" O   VAL B 273 "
    ideal  model  delta    sigma   weight residual
    1.237  1.219  0.018 1.19e-02 7.06e+03 2.27e+00
  bond pdb=" CA  VAL B 273 "
       pdb=" CB  VAL B 273 "
    ideal  model  delta    sigma   weight residual
    1.540  1.557 -0.018 1.29e-02 6.01e+03 1.90e+00
  bond pdb=" C   TYR C 248 "
       pdb=" O   TYR C 248 "
    ideal  model  delta    sigma   weight residual
    1.236  1.221  0.015 1.15e-02 7.56e+03 1.77e+00
  bond pdb=" C   LEU A 270 "
       pdb=" O   LEU A 270 "
    ideal  model  delta    sigma   weight residual
    1.236  1.220  0.016 1.21e-02 6.83e+03 1.71e+00
  bond pdb=" C   VAL A 249 "
       pdb=" O   VAL A 249 "
    ideal  model  delta    sigma   weight residual
    1.237  1.222  0.015 1.17e-02 7.31e+03 1.61e+00
  ... (remaining 5029 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.63: 6801
        2.63 -     5.26: 65
        5.26 -     7.89: 7
        7.89 -    10.52: 3
       10.52 -    13.15: 3
  Bond angle restraints: 6879
  Sorted by residual:
  angle pdb=" C   VAL A 287 "
        pdb=" N   LEU A 288 "
        pdb=" CA  LEU A 288 "
      ideal   model   delta    sigma   weight residual
     122.93  136.08  -13.15 1.45e+00 4.76e-01 8.23e+01
  angle pdb=" C   ASN A 282 "
        pdb=" N   LEU A 283 "
        pdb=" CA  LEU A 283 "
      ideal   model   delta    sigma   weight residual
     120.28  131.22  -10.94 1.34e+00 5.57e-01 6.67e+01
  angle pdb=" N   LEU B 253 "
        pdb=" CA  LEU B 253 "
        pdb=" C   LEU B 253 "
      ideal   model   delta    sigma   weight residual
     111.07  105.54    5.53 1.07e+00 8.73e-01 2.67e+01
  angle pdb=" N   LEU A 270 "
        pdb=" CA  LEU A 270 "
        pdb=" C   LEU A 270 "
      ideal   model   delta    sigma   weight residual
     111.37  119.28   -7.91 1.64e+00 3.72e-01 2.33e+01
  angle pdb=" N   LYS B 267 "
        pdb=" CA  LYS B 267 "
        pdb=" C   LYS B 267 "
      ideal   model   delta    sigma   weight residual
     108.45  113.49   -5.04 1.26e+00 6.30e-01 1.60e+01
  ... (remaining 6874 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 2649
       17.77 -    35.55: 143
       35.55 -    53.32: 47
       53.32 -    71.09: 18
       71.09 -    88.87: 8
  Dihedral angle restraints: 2865
    sinusoidal: 1017
      harmonic: 1848
  Sorted by residual:
  dihedral pdb=" CA  ASN B 284 "
           pdb=" C   ASN B 284 "
           pdb=" N   GLY B 285 "
           pdb=" CA  GLY B 285 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.22  -19.78     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" C   ASN B 290 "
           pdb=" N   ASN B 290 "
           pdb=" CA  ASN B 290 "
           pdb=" CB  ASN B 290 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.12    9.52     0      2.50e+00 1.60e-01 1.45e+01
  dihedral pdb=" C   VAL B 273 "
           pdb=" N   VAL B 273 "
           pdb=" CA  VAL B 273 "
           pdb=" CB  VAL B 273 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -131.19    9.19     0      2.50e+00 1.60e-01 1.35e+01
  ... (remaining 2862 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.345: 793
       0.345 -    0.689: 4
       0.689 -    1.034: 0
       1.034 -    1.379: 0
       1.379 -    1.723: 1
  Chirality restraints: 798
  Sorted by residual:
  chirality pdb=" CG  LEU B 283 "
            pdb=" CB  LEU B 283 "
            pdb=" CD1 LEU B 283 "
            pdb=" CD2 LEU B 283 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.87   -1.72 2.00e-01 2.50e+01 7.42e+01
  chirality pdb=" CA  LEU B 288 "
            pdb=" N   LEU B 288 "
            pdb=" C   LEU B 288 "
            pdb=" CB  LEU B 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.08e+00
  chirality pdb=" CA  LEU A 288 "
            pdb=" N   LEU A 288 "
            pdb=" C   LEU A 288 "
            pdb=" CB  LEU A 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.22e+00
  ... (remaining 795 not shown)

  Planarity restraints: 897
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 273 "   -0.005 2.00e-02 2.50e+03   1.11e-02 1.22e+00
        pdb=" C   VAL B 273 "    0.019 2.00e-02 2.50e+03
        pdb=" O   VAL B 273 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   ASN B 274 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 412 "   -0.016 5.00e-02 4.00e+02   2.49e-02 9.94e-01
        pdb=" N   PRO A 413 "    0.043 5.00e-02 4.00e+02
        pdb=" CA  PRO A 413 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 413 "   -0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 249 "   -0.005 2.00e-02 2.50e+03   9.15e-03 8.37e-01
        pdb=" C   VAL A 249 "    0.016 2.00e-02 2.50e+03
        pdb=" O   VAL A 249 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   ASN A 250 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 894 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.52: 87
        2.52 -     3.12: 4191
        3.12 -     3.71: 8315
        3.71 -     4.31: 11712
        4.31 -     4.90: 19104
  Nonbonded interactions: 43409
  Sorted by model distance:
  nonbonded pdb=" O   GLN C 276 "
            pdb=" OG  SER C 279 "
     model   vdw
     1.931 3.040
  nonbonded pdb=" O   GLU B 365 "
            pdb=" OH  TYR B 369 "
     model   vdw
     2.001 3.040
  nonbonded pdb=" OG1 THR A 340 "
            pdb=" OD1 ASN A 436 "
     model   vdw
     2.019 3.040
  nonbonded pdb=" OG  SER A 333 "
            pdb=" OG  SER A 335 "
     model   vdw
     2.039 3.040
  nonbonded pdb=" OG1 THR B 303 "
            pdb=" OG1 THR C 292 "
     model   vdw
     2.050 3.040
  ... (remaining 43404 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'
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.290
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:    9.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
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      :  0.003   0.029   5034  Z= 0.197
  Angle     :  0.704  13.153   6879  Z= 0.417
  Chirality :  0.081   1.723    798
  Planarity :  0.003   0.030    897
  Dihedral  : 14.469  88.867   1695
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.71 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  7.55 %
    Allowed  :  6.81 %
    Favored  : 85.64 %
  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 aren not related in a simple way.
  whole: -1.09 (0.32), residues: 648
  helix: -0.53 (0.41), residues: 132
  sheet:  0.26 (0.36), residues: 222
  loop : -1.58 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 376 
 TYR   0.007   0.001   TYR A 387 
 PHE   0.015   0.001   PHE B 321 
 TRP   0.007   0.001   TRP C 361 
 HIS   0.002   0.001   HIS C 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 5034)
  covalent geometry    : angle       0.70432 ( 6879)
  hydrogen bonds       : bond        0.25587 (  219)
  hydrogen bonds       : angle       9.35442 (  609)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 91
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 SER cc_start: 0.9393 (m) cc_final: 0.9031 (p)
REVERT: A  344 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7117 (m-40)
REVERT: A  365 GLU cc_start: 0.8762 (tt0) cc_final: 0.8146 (tt0)
REVERT: B  391 LEU cc_start: 0.8550 (mp) cc_final: 0.8014 (tt)
REVERT: B  419 LEU cc_start: 0.7695 (mp) cc_final: 0.7342 (tt)
REVERT: C  365 GLU cc_start: 0.8504 (tt0) cc_final: 0.8298 (mm-30)
REVERT: C  371 ILE cc_start: 0.8179 (mm) cc_final: 0.7832 (mp)
REVERT: C  425 LEU cc_start: 0.8647 (mt) cc_final: 0.8371 (mt)
  outliers start: 41
  outliers final: 7
  residues processed: 115
  average time/residue: 0.0914
  time to fit residues: 13.0541
Evaluate side-chains
  62 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 LYS
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  344 ASN
Chi-restraints excluded: chain B residue  247 SER
Chi-restraints excluded: chain B residue  261 ASP
Chi-restraints excluded: chain B residue  267 LYS
Chi-restraints excluded: chain B residue  282 ASN
Chi-restraints excluded: chain C residue  260 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 48 optimal weight:   20.0000
   chunk 56 optimal weight:    9.9990
   chunk 26 optimal weight:   30.0000
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    6.9990
   chunk 61 optimal weight:    7.9990
   chunk 32 optimal weight:    9.9990
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 250 ASN
B 440 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.046931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.038009 restraints weight = 39953.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.039210 restraints weight = 25870.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.040078 restraints weight = 18702.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.040705 restraints weight = 14454.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.041190 restraints weight = 11854.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.3189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   5034  Z= 0.214
  Angle     :  0.700   9.381   6879  Z= 0.365
  Chirality :  0.047   0.173    798
  Planarity :  0.004   0.030    897
  Dihedral  :  6.949  57.288    724
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 12.52 %
    Favored  : 83.79 %
  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 aren not related in a simple way.
  whole: -0.61 (0.33), residues: 648
  helix:  0.43 (0.43), residues: 135
  sheet:  0.23 (0.35), residues: 231
  loop : -1.33 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 318 
 TYR   0.020   0.002   TYR A 248 
 PHE   0.020   0.002   PHE B 434 
 TRP   0.011   0.001   TRP A 361 
 HIS   0.004   0.001   HIS B 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 5034)
  covalent geometry    : angle       0.69989 ( 6879)
  hydrogen bonds       : bond        0.04855 (  219)
  hydrogen bonds       : angle       6.50541 (  609)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 57
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  365 GLU cc_start: 0.8677 (tt0) cc_final: 0.8119 (tt0)
REVERT: C  412 TYR cc_start: 0.8963 (m-80) cc_final: 0.8557 (m-80)
  outliers start: 20
  outliers final: 13
  residues processed: 68
  average time/residue: 0.0636
  time to fit residues: 5.8558
Evaluate side-chains
  56 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 43
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 LYS
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  267 LYS
Chi-restraints excluded: chain B residue  282 ASN
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  393 PHE
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain C residue  267 LYS
Chi-restraints excluded: chain C residue  269 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 21 optimal weight:   20.0000
   chunk 27 optimal weight:    9.9990
   chunk 56 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 51 optimal weight:    9.9990
   chunk 59 optimal weight:    5.9990
   chunk 37 optimal weight:    0.0470
   chunk 7 optimal weight:    9.9990
   chunk 4 optimal weight:    4.9990
   chunk 30 optimal weight:   20.0000
   chunk 38 optimal weight:    6.9990
   overall best weight:    5.0086

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

Flipped N/Q/H residues before XYZ refinement:
A 310 HIS
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 310 HIS
C 409 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.045004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.036355 restraints weight = 38769.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.037529 restraints weight = 24720.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.038382 restraints weight = 17731.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.038987 restraints weight = 13671.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.039457 restraints weight = 11158.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.4260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5034  Z= 0.185
  Angle     :  0.664  10.012   6879  Z= 0.340
  Chirality :  0.045   0.225    798
  Planarity :  0.004   0.081    897
  Dihedral  :  6.309  53.747    717
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 15.42
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.02 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 13.26 %
    Favored  : 82.87 %
  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 aren not related in a simple way.
  whole: -0.37 (0.33), residues: 648
  helix:  1.16 (0.44), residues: 135
  sheet:  0.16 (0.35), residues: 231
  loop : -1.27 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 376 
 TYR   0.020   0.002   TYR A 369 
 PHE   0.017   0.002   PHE A 393 
 TRP   0.012   0.001   TRP A 361 
 HIS   0.003   0.001   HIS C 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 5034)
  covalent geometry    : angle       0.66419 ( 6879)
  hydrogen bonds       : bond        0.04161 (  219)
  hydrogen bonds       : angle       5.83248 (  609)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 43
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 SER cc_start: 0.9554 (m) cc_final: 0.9309 (p)
REVERT: B  263 LEU cc_start: 0.9433 (mt) cc_final: 0.9139 (pp)
REVERT: B  365 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8249 (tm-30)
REVERT: C  365 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7013 (mm-30)
REVERT: C  371 ILE cc_start: 0.7540 (mm) cc_final: 0.6959 (mp)
REVERT: C  412 TYR cc_start: 0.8922 (m-80) cc_final: 0.8578 (m-80)
  outliers start: 21
  outliers final: 15
  residues processed: 57
  average time/residue: 0.0590
  time to fit residues: 4.7423
Evaluate side-chains
  55 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 40
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 LYS
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  393 PHE
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  267 LYS
Chi-restraints excluded: chain B residue  282 ASN
Chi-restraints excluded: chain C residue  267 LYS
Chi-restraints excluded: chain C residue  269 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 39 optimal weight:    6.9990
   chunk 33 optimal weight:   20.0000
   chunk 2 optimal weight:    1.9990
   chunk 37 optimal weight:   10.0000
   chunk 59 optimal weight:    5.9990
   chunk 20 optimal weight:   20.0000
   chunk 9 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 16 optimal weight:    9.9990
   chunk 40 optimal weight:    8.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.043282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.034797 restraints weight = 39452.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.035951 restraints weight = 24866.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.036799 restraints weight = 17696.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.037375 restraints weight = 13580.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.037822 restraints weight = 11097.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.4885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5034  Z= 0.198
  Angle     :  0.626   8.464   6879  Z= 0.322
  Chirality :  0.043   0.147    798
  Planarity :  0.004   0.068    897
  Dihedral  :  6.234  51.008    717
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 15.94
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.64 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 14.36 %
    Favored  : 81.77 %
  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 aren not related in a simple way.
  whole: -0.29 (0.33), residues: 648
  helix:  1.28 (0.45), residues: 135
  sheet:  0.21 (0.36), residues: 225
  loop : -1.23 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 376 
 TYR   0.018   0.002   TYR A 417 
 PHE   0.018   0.002   PHE B 321 
 TRP   0.008   0.001   TRP A 361 
 HIS   0.004   0.001   HIS A 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 5034)
  covalent geometry    : angle       0.62581 ( 6879)
  hydrogen bonds       : bond        0.03733 (  219)
  hydrogen bonds       : angle       5.64882 (  609)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 41
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 SER cc_start: 0.9579 (m) cc_final: 0.9326 (p)
REVERT: A  365 GLU cc_start: 0.8635 (tt0) cc_final: 0.8060 (tt0)
REVERT: B  365 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8380 (tm-30)
REVERT: B  415 PHE cc_start: 0.9152 (m-10) cc_final: 0.8813 (m-10)
REVERT: C  365 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7208 (mm-30)
REVERT: C  412 TYR cc_start: 0.9004 (m-80) cc_final: 0.8718 (m-80)
  outliers start: 21
  outliers final: 18
  residues processed: 54
  average time/residue: 0.0555
  time to fit residues: 4.3264
Evaluate side-chains
  57 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 39
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  393 PHE
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  434 PHE
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  267 LYS
Chi-restraints excluded: chain B residue  282 ASN
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  447 TYR
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain C residue  267 LYS
Chi-restraints excluded: chain C residue  269 ASP
Chi-restraints excluded: chain C residue  370 LEU
Chi-restraints excluded: chain C residue  409 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 53 optimal weight:    8.9990
   chunk 35 optimal weight:    5.9990
   chunk 51 optimal weight:    8.9990
   chunk 8 optimal weight:   30.0000
   chunk 40 optimal weight:    8.9990
   chunk 33 optimal weight:   20.0000
   chunk 45 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   overall best weight:    4.1588

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

Flipped N/Q/H residues before XYZ refinement:
B 403 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.042769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.034366 restraints weight = 39325.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.035559 restraints weight = 24286.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.036391 restraints weight = 17073.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.037019 restraints weight = 13042.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.037452 restraints weight = 10534.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.5289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5034  Z= 0.154
  Angle     :  0.613  14.174   6879  Z= 0.310
  Chirality :  0.043   0.151    798
  Planarity :  0.003   0.062    897
  Dihedral  :  5.818  46.719    713
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 14.28
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.71 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 15.47 %
    Favored  : 80.48 %
  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 aren not related in a simple way.
  whole: -0.25 (0.34), residues: 648
  helix:  1.41 (0.45), residues: 135
  sheet:  0.18 (0.36), residues: 223
  loop : -1.20 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 312 
 TYR   0.021   0.002   TYR A 387 
 PHE   0.016   0.001   PHE B 321 
 TRP   0.006   0.001   TRP B 421 
 HIS   0.003   0.001   HIS A 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 5034)
  covalent geometry    : angle       0.61347 ( 6879)
  hydrogen bonds       : bond        0.03513 (  219)
  hydrogen bonds       : angle       5.52641 (  609)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 42
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 SER cc_start: 0.9591 (m) cc_final: 0.9340 (p)
REVERT: B  365 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8370 (tm-30)
REVERT: B  415 PHE cc_start: 0.9169 (m-10) cc_final: 0.8569 (m-10)
REVERT: C  365 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7542 (mm-30)
REVERT: C  371 ILE cc_start: 0.7523 (mm) cc_final: 0.7011 (mp)
REVERT: C  412 TYR cc_start: 0.8966 (m-80) cc_final: 0.8707 (m-80)
  outliers start: 22
  outliers final: 17
  residues processed: 56
  average time/residue: 0.0562
  time to fit residues: 4.5468
Evaluate side-chains
  56 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 39
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  393 PHE
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  434 PHE
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  267 LYS
Chi-restraints excluded: chain B residue  282 ASN
Chi-restraints excluded: chain B residue  447 TYR
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain C residue  265 SER
Chi-restraints excluded: chain C residue  269 ASP
Chi-restraints excluded: chain C residue  370 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 38 optimal weight:    9.9990
   chunk 40 optimal weight:    8.9990
   chunk 50 optimal weight:   10.0000
   chunk 29 optimal weight:    9.9990
   chunk 11 optimal weight:    8.9990
   chunk 57 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 9 optimal weight:   10.0000
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.041075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.032878 restraints weight = 40780.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.034030 restraints weight = 24835.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.034851 restraints weight = 17344.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.035448 restraints weight = 13160.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.035869 restraints weight = 10582.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.5837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   5034  Z= 0.201
  Angle     :  0.664  11.926   6879  Z= 0.337
  Chirality :  0.043   0.193    798
  Planarity :  0.004   0.057    897
  Dihedral  :  5.920  47.576    713
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 15.73
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.94 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 16.02 %
    Favored  : 80.29 %
  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 aren not related in a simple way.
  whole: -0.55 (0.33), residues: 648
  helix:  1.05 (0.45), residues: 135
  sheet: -0.04 (0.36), residues: 213
  loop : -1.24 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 376 
 TYR   0.034   0.002   TYR A 387 
 PHE   0.020   0.002   PHE A 434 
 TRP   0.008   0.001   TRP A 352 
 HIS   0.004   0.001   HIS A 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 5034)
  covalent geometry    : angle       0.66432 ( 6879)
  hydrogen bonds       : bond        0.03633 (  219)
  hydrogen bonds       : angle       5.66829 (  609)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 37
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  256 ASP cc_start: 0.9256 (m-30) cc_final: 0.8979 (p0)
REVERT: B  267 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8434 (mmtt)
REVERT: C  365 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7586 (mm-30)
REVERT: C  412 TYR cc_start: 0.9009 (m-80) cc_final: 0.8774 (m-80)
  outliers start: 20
  outliers final: 14
  residues processed: 49
  average time/residue: 0.0489
  time to fit residues: 3.7276
Evaluate side-chains
  50 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 35
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  393 PHE
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  434 PHE
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  267 LYS
Chi-restraints excluded: chain B residue  282 ASN
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain C residue  269 ASP
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  370 LEU
Chi-restraints excluded: chain C residue  409 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 48 optimal weight:    9.9990
   chunk 14 optimal weight:    7.9990
   chunk 49 optimal weight:    6.9990
   chunk 62 optimal weight:   10.0000
   chunk 9 optimal weight:   10.0000
   chunk 61 optimal weight:   10.0000
   chunk 18 optimal weight:   10.0000
   chunk 44 optimal weight:    5.9990
   chunk 12 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    4.1990

-------------------------------------------------------------------------------
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 = 0.3256 r_free = 0.3256 target = 0.041248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.033025 restraints weight = 39378.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.034171 restraints weight = 23904.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.034998 restraints weight = 16706.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.035608 restraints weight = 12629.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.036026 restraints weight = 10175.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.6091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5034  Z= 0.153
  Angle     :  0.652  11.708   6879  Z= 0.323
  Chirality :  0.044   0.233    798
  Planarity :  0.004   0.071    897
  Dihedral  :  5.556  47.325    711
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 14.59
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.56 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 16.57 %
    Favored  : 79.93 %
  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 aren not related in a simple way.
  whole: -0.47 (0.33), residues: 648
  helix:  1.15 (0.44), residues: 135
  sheet:  0.10 (0.37), residues: 206
  loop : -1.26 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 376 
 TYR   0.021   0.002   TYR A 387 
 PHE   0.015   0.001   PHE A 434 
 TRP   0.006   0.001   TRP B 352 
 HIS   0.003   0.001   HIS A 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 5034)
  covalent geometry    : angle       0.65163 ( 6879)
  hydrogen bonds       : bond        0.03325 (  219)
  hydrogen bonds       : angle       5.49666 (  609)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 38
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 SER cc_start: 0.9601 (m) cc_final: 0.9381 (p)
REVERT: B  256 ASP cc_start: 0.9293 (m-30) cc_final: 0.9004 (p0)
REVERT: B  267 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8500 (mmtt)
REVERT: B  365 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8205 (tm-30)
REVERT: C  371 ILE cc_start: 0.7539 (mm) cc_final: 0.6992 (mp)
REVERT: C  412 TYR cc_start: 0.9020 (m-80) cc_final: 0.8759 (m-80)
  outliers start: 19
  outliers final: 11
  residues processed: 49
  average time/residue: 0.0568
  time to fit residues: 4.0438
Evaluate side-chains
  44 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 32
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  393 PHE
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  267 LYS
Chi-restraints excluded: chain B residue  282 ASN
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  370 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 8 optimal weight:   20.0000
   chunk 42 optimal weight:    7.9990
   chunk 59 optimal weight:   20.0000
   chunk 54 optimal weight:    5.9990
   chunk 17 optimal weight:   10.0000
   chunk 58 optimal weight:   20.0000
   chunk 40 optimal weight:   10.0000
   chunk 28 optimal weight:    9.9990
   chunk 50 optimal weight:    9.9990
   chunk 44 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   overall best weight:    5.3990

-------------------------------------------------------------------------------
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 = 0.3231 r_free = 0.3231 target = 0.040301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.032311 restraints weight = 40004.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.033478 restraints weight = 23716.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.034280 restraints weight = 16317.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.034845 restraints weight = 12291.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.035280 restraints weight = 9908.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.6487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5034  Z= 0.180
  Angle     :  0.666  11.472   6879  Z= 0.336
  Chirality :  0.044   0.227    798
  Planarity :  0.004   0.076    897
  Dihedral  :  5.595  48.183    711
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 15.32
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.02 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 18.78 %
    Favored  : 78.64 %
  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 aren not related in a simple way.
  whole: -0.50 (0.33), residues: 648
  helix:  1.17 (0.44), residues: 135
  sheet:  0.07 (0.36), residues: 206
  loop : -1.29 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 407 
 TYR   0.030   0.002   TYR A 387 
 PHE   0.015   0.002   PHE B 415 
 TRP   0.013   0.002   TRP C 352 
 HIS   0.004   0.001   HIS A 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 5034)
  covalent geometry    : angle       0.66645 ( 6879)
  hydrogen bonds       : bond        0.03394 (  219)
  hydrogen bonds       : angle       5.45474 (  609)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 30
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 SER cc_start: 0.9614 (m) cc_final: 0.9404 (p)
REVERT: B  256 ASP cc_start: 0.9306 (m-30) cc_final: 0.8978 (p0)
REVERT: B  267 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8697 (mmtt)
REVERT: B  365 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8212 (tm-30)
REVERT: C  412 TYR cc_start: 0.8961 (m-80) cc_final: 0.8681 (m-80)
  outliers start: 14
  outliers final: 11
  residues processed: 38
  average time/residue: 0.0464
  time to fit residues: 2.7990
Evaluate side-chains
  41 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 29
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  393 PHE
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  267 LYS
Chi-restraints excluded: chain B residue  282 ASN
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  370 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 35 optimal weight:   20.0000
   chunk 15 optimal weight:    5.9990
   chunk 38 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 11 optimal weight:    0.9990
   chunk 4 optimal weight:    7.9990
   chunk 56 optimal weight:    9.9990
   chunk 18 optimal weight:    5.9990
   chunk 23 optimal weight:    7.9990
   chunk 17 optimal weight:    2.9990
   chunk 60 optimal weight:   20.0000
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** C 328 GLN ** 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 = 0.3205 r_free = 0.3205 target = 0.039553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.031594 restraints weight = 39843.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.032711 restraints weight = 23927.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.033501 restraints weight = 16667.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.034067 restraints weight = 12674.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.034481 restraints weight = 10240.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.6919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5034  Z= 0.161
  Angle     :  0.639  12.588   6879  Z= 0.321
  Chirality :  0.043   0.198    798
  Planarity :  0.004   0.074    897
  Dihedral  :  5.452  49.198    711
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 14.07
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.09 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 19.15 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.46 (0.33), residues: 648
  helix:  1.15 (0.44), residues: 135
  sheet:  0.08 (0.36), residues: 206
  loop : -1.24 (0.36), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 376 
 TYR   0.027   0.002   TYR A 387 
 PHE   0.014   0.002   PHE B 321 
 TRP   0.007   0.001   TRP B 421 
 HIS   0.003   0.001   HIS A 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 5034)
  covalent geometry    : angle       0.63927 ( 6879)
  hydrogen bonds       : bond        0.03320 (  219)
  hydrogen bonds       : angle       5.31657 (  609)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 31
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  368 THR cc_start: 0.9194 (OUTLIER) cc_final: 0.8895 (p)
REVERT: B  256 ASP cc_start: 0.9297 (m-30) cc_final: 0.9004 (p0)
REVERT: B  267 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8692 (mmtt)
REVERT: B  365 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8214 (tm-30)
REVERT: C  412 TYR cc_start: 0.9006 (m-80) cc_final: 0.8742 (m-80)
  outliers start: 14
  outliers final: 10
  residues processed: 39
  average time/residue: 0.0458
  time to fit residues: 2.8437
Evaluate side-chains
  41 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 29
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  393 PHE
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  267 LYS
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  370 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 17 optimal weight:    8.9990
   chunk 9 optimal weight:    7.9990
   chunk 16 optimal weight:    8.9990
   chunk 23 optimal weight:    9.9990
   chunk 7 optimal weight:    5.9990
   chunk 40 optimal weight:    6.9990
   chunk 36 optimal weight:    7.9990
   chunk 28 optimal weight:   10.0000
   chunk 19 optimal weight:   10.0000
   chunk 14 optimal weight:    8.9990
   chunk 29 optimal weight:    8.9990
   overall best weight:    7.5990

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

Flipped N/Q/H residues before XYZ refinement:
** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 440 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.037622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.029980 restraints weight = 41940.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.031065 restraints weight = 24891.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.031809 restraints weight = 17178.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.032349 restraints weight = 13054.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.032729 restraints weight = 10524.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.7460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   5034  Z= 0.242
  Angle     :  0.694  11.943   6879  Z= 0.357
  Chirality :  0.044   0.211    798
  Planarity :  0.005   0.093    897
  Dihedral  :  5.694  53.125    709
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 18.32
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.48 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 19.34 %
    Favored  : 78.08 %
  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 aren not related in a simple way.
  whole: -0.77 (0.33), residues: 648
  helix:  0.80 (0.43), residues: 135
  sheet: -0.13 (0.36), residues: 212
  loop : -1.39 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 376 
 TYR   0.024   0.002   TYR A 387 
 PHE   0.015   0.002   PHE B 321 
 TRP   0.018   0.002   TRP A 352 
 HIS   0.006   0.002   HIS A 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 ( 5034)
  covalent geometry    : angle       0.69364 ( 6879)
  hydrogen bonds       : bond        0.03817 (  219)
  hydrogen bonds       : angle       5.62822 (  609)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 26
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
REVERT: A  365 GLU cc_start: 0.8445 (tt0) cc_final: 0.7779 (tt0)
REVERT: A  368 THR cc_start: 0.9239 (OUTLIER) cc_final: 0.8903 (p)
REVERT: B  256 ASP cc_start: 0.9289 (m-30) cc_final: 0.9021 (p0)
REVERT: B  365 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8211 (tm-30)
  outliers start: 14
  outliers final: 12
  residues processed: 34
  average time/residue: 0.0515
  time to fit residues: 2.7554
Evaluate side-chains
  39 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 26
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  393 PHE
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  267 LYS
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain C residue  265 SER
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  370 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 31 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   chunk 36 optimal weight:    1.9990
   chunk 8 optimal weight:   20.0000
   chunk 2 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 11 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   chunk 22 optimal weight:    9.9990
   chunk 34 optimal weight:   30.0000
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** C 328 GLN ** 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 = 0.3166 r_free = 0.3166 target = 0.038320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.030560 restraints weight = 40744.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.031691 restraints weight = 23856.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.032480 restraints weight = 16357.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.033013 restraints weight = 12312.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.033436 restraints weight = 9911.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8625
moved from start:          0.7577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5034  Z= 0.156
  Angle     :  0.632  12.534   6879  Z= 0.320
  Chirality :  0.043   0.183    798
  Planarity :  0.004   0.079    897
  Dihedral  :  5.450  50.726    709
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 14.49
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.25 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 19.34 %
    Favored  : 78.45 %
  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 aren not related in a simple way.
  whole: -0.56 (0.33), residues: 648
  helix:  1.05 (0.43), residues: 135
  sheet: -0.06 (0.35), residues: 214
  loop : -1.25 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 376 
 TYR   0.023   0.002   TYR A 387 
 PHE   0.012   0.002   PHE B 321 
 TRP   0.007   0.001   TRP B 421 
 HIS   0.003   0.001   HIS A 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 5034)
  covalent geometry    : angle       0.63209 ( 6879)
  hydrogen bonds       : bond        0.03420 (  219)
  hydrogen bonds       : angle       5.37426 (  609)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 974.81 seconds
wall clock time: 17 minutes 35.59 seconds (1055.59 seconds total)